Methods of distinguishing ischemic stroke from intracerebral hemorrhage

ABSTRACT

Provided are compositions and methods for differentiating and diagnosing ischemic stroke and subgroups thereof (e.g., cardioembolic stroke, large vessel stroke, atherothrombotic stroke, lacunar stroke) from intracerebral hemorrhage.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is the U.S. national phase under 35 U.S.C. § 371 of Intl. Appl. No. PCT/US2016/031028, which claims the benefit under 35 U.S.C. § 119(e) of U.S. Provisional Application No. 62/159,502, filed on May 11, 2015, which are hereby incorporated herein by reference in their entireties for all purposes.

STATEMENT OF GOVERNMENTAL SUPPORT

This invention was made with Government support under Grant Nos. NS075035, NS079153 and AG042292, all awarded by the National Institutes of Health. The government has certain rights in this invention.

FIELD

Provided are compositions and methods for differentiating and diagnosing ischemic stroke and subgroups thereof (e.g., cardioembolic stroke, large vessel stroke, atherothrombotic stroke, lacunar stroke) from intracerebral hemorrhage.

BACKGROUND

Clinicians diagnose stroke based on patient history, neurological exams and brain imaging. This can be difficult and distinguishing ischemic stroke (IS) from hemorrhage can be challenging when imaging is unavailable in the acute setting.

Blood transcriptomes have provided insights into the immune response following human stroke and show promise as diagnostic biomarkers [1-6]. However, these studies have investigated only a proportion of the protein coding transcriptome, since they have used 3′-biased microarrays to measure blood mRNA expression [1-6]. Though these studies provided proof-of-principle, the vast complexity of the stroke transcriptome which is comprised of alternatively spliced isoforms remains unstudied in stroke. The importance of alternative splicing (AS) in stroke is supported by increasing evidence implicating AS in the pathogenesis of many diseases [7, 8].

AS is the process whereby exons from a single gene are included or excluded in the final mRNA transcript (FIG. 1). A single gene produces several AS isoforms with specific functions in different cells, tissues, developmental stages and disease states. Thus, the ˜20,000 known genes code for >250,000 different mRNAs and proteins. Differential alternative splicing (DAS) is AS that differs between groups. We investigated whether DAS would vary for different IS causes (cardioembolic, large vessel and lacunar) compared to intracerebral hemorrhage (ICH) and controls. Therefore, we used RNA sequencing (RNA-Seq) to measure DAS in whole blood samples of humans with ICH and with different causes of IS and compared these to controls. RNA-Seq is a new technology that allows for estimation of expression of each splice variant (FIG. 1), a significant advance over previously used technologies in stroke. To date, there have been no RNA-Seq studies for AS markers of stroke etiology, or for distinguishing between ischemic stroke and ICH either in humans or in animal models.

SUMMARY

In one aspect, provided are methods for diagnosing cardioembolic ischemic stroke (CE IS) or a predisposition for experiencing CE IS. In some embodiments, the methods comprise determining a level of exon or splice variant usage or expression of a plurality of biomarkers in a biological sample from a patient, wherein an increase of the level of exon usage or expression compared to a control indicates that the patient has suffered or is at risk of experiencing CE IS, wherein the plurality of exons or splice variants of the biomarkers is selected from the biomarkers set forth in Table 1A, thereby diagnosing CE IS or a predisposition for experiencing CE IS.

In a further aspect, provided are methods for diagnosing large vessel ischemic stroke (LV IS) or a predisposition for experiencing LV IS. In some embodiments, the methods comprise determining a level of exon or splice variant usage or expression of a plurality of biomarkers in a biological sample from a patient, wherein an increase of the level of exon usage or expression compared to a control indicates that the patient has suffered or is at risk of experiencing LV IS, wherein the plurality of exons or splice variants of the biomarkers is selected from the biomarkers set forth in Table 1B, thereby diagnosing LV IS or a predisposition for experiencing LV IS.

In a further aspect, provided are methods for diagnosing lacunar ischemic stroke (L IS) or a predisposition for experiencing L IS. In some embodiments, the methods comprise determining a level of exon or splice variant usage or expression of a plurality of biomarkers in a biological sample from a patient, wherein an increase of the level of exon usage or expression compared to a control indicates that the patient has suffered or is at risk of experiencing L IS, wherein the plurality of exons or splice variants of the biomarkers is selected from the biomarkers set forth in Table 1C, thereby diagnosing L IS or a predisposition for experiencing L IS.

In a further aspect, provided are methods for diagnosing intracerebral hemorrhage (ICH) or a predisposition for experiencing ICH. In some embodiments, the methods comprise determining a level of exon usage or expression of a plurality of biomarkers in a biological sample from a patient, wherein an increase of the level of exon or splice variant usage or expression compared to a control indicates that the patient has suffered or is at risk of experiencing ICH, wherein the plurality of exons or splice variants of the biomarkers is selected from the biomarkers set forth in Table 1D, thereby diagnosing ICH or a predisposition for experiencing ICH.

In a further aspect, provided are methods of differentiating between ischemic stroke (IS) from intracerebral hemorrhage (ICH). In some embodiments, the methods comprise determining a level of exon or splice variant usage or expression of a plurality of biomarkers set forth in Table 1A, a plurality of biomarkers set forth in Table 1B, a plurality of biomarkers set forth in Table 1C, and a plurality of biomarkers set forth in Table 1D, in a biological sample from a patient, wherein detecting:

a) an increase of the level of exon or splice variant usage or expression of a plurality of exons of the biomarkers set forth in Table 1A compared to a control indicates that the patient has suffered or is at risk of experiencing cardioembolic ischemic stroke (CE IS);

b) an increase of the level of exon or splice variant usage or expression of a plurality of exons of the biomarkers set forth in Table 1B compared to a control indicates that the patient has suffered or is at risk of experiencing large vessel ischemic stroke (LV IS);

c) an increase of the level of exon or splice variant usage or expression of a plurality of exons of the biomarkers set forth in Table 1C compared to a control indicates that the patient has suffered or is at risk of experiencing lacunar ischemic stroke (L IS); and

d) an increase of the level of exon or splice variant usage or expression of a plurality of exons of the biomarkers set forth in Table 1D compared to a control indicates that the patient has suffered or is at risk of experiencing ICH; thereby differentiating between ischemic stroke (IS) from ICH.

With respect to embodiments of the methods, in some embodiments, the determining step is performed at 3 or more hours after a suspected ischemic stroke or ICH. In some embodiments, the determining step is performed at 3 or fewer hours after a suspected ischemic stroke or ICH. In some embodiments, the determining step is performed at 24 or fewer hours after a suspected ischemic stroke or ICH. In some embodiments, the determining step is performed at least 24 hours after a suspected ischemic stroke or ICH. In some embodiments, the level of expression of the biomarker is determined at the transcriptional level. In varying embodiments, the level of expression is determined by detecting hybridization of a nucleic acid probe to gene transcripts of the biomarkers in the biological sample. In varying embodiments, the hybridization step is performed on a nucleic acid microarray chip. In varying embodiments, the hybridization step is performed in a microfluidics assay plate. In varying embodiments, the level of expression is determined by direct RNA sequencing of gene transcripts of the biomarkers. In varying embodiments, the level of expression is determined by amplification of gene transcripts of the biomarkers. In varying embodiments, the amplification reaction is a polymerase chain reaction (PCR). In varying embodiments, the amplification reaction comprises quantitative reverse transcription polymerase chain reaction (qRT-PCR). In varying embodiments, the amplification reaction comprises reverse transcription (RT) followed by a ligase detection reaction (LDR) with single-pair fluorescence resonance energy transfer (spFRET) (RT-LDR/spFRET). In varying embodiments, the level of expression of the biomarker isoform is determined at the protein level. In varying embodiments, the level of expression of at least 15 biomarkers, e.g., at least 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100 biomarkers, or all listed biomarkers in the identified Table (e.g., Table 1A, Table 1B, Table 1C, Table 1D and/or Table 1E), are determined. In varying embodiments, the methods further comprise the step of obtaining a biological sample. In varying embodiments, the biological sample is blood, serum or plasma. In varying embodiments, the increased level of exon usage of a biomarker is at least about 1.2-fold in comparison to a control. In varying embodiments, the control is the expression level of the same biomarker in an individual with no history of stroke, heart attack, or peripheral vascular disease. In varying embodiments, the control is a threshold level of expression representative of a population of individuals with no history of stroke, heart attack, peripheral vascular disease. In varying embodiments, the individual or the population of individuals has at least one vascular risk factor. In varying embodiments, the control is an individual or population of individuals who have increased expression of one or more biomarkers set forth in Table 1E. In varying embodiments, the methods further comprise the step of providing a diagnosis for ischemic stroke/ICH to the patient based on the determination and identification of the level of expression of the set of ischemic stroke/ICH biomarkers. In varying embodiments, the methods further comprise the step of providing an appropriate treatment or prevention regime for ischemic stroke/ICH to the patient. In varying embodiments, the subject has experienced or is suspected of having experienced ischemic stroke or ICH. In varying embodiments, if the patient has experienced or has a predisposition to experience ischemic stroke or ICH, further comprising the step of determining the cause or risk of the ischemic stroke or ICH

In a further aspect, provided are solid supports. In varying embodiments, the solid supports comprise a plurality of oligonucleotide probes that hybridize to a plurality of the biomarkers set forth in Table 1A. In varying embodiments, the solid supports comprise a plurality of oligonucleotide probes that hybridize to a plurality of the biomarkers set forth in Table 1B. In varying embodiments, the solid supports comprise a plurality of oligonucleotide probes that hybridize to a plurality of the biomarkers set forth in Table 1C. In varying embodiments, the solid supports comprise a plurality of oligonucleotide probes that hybridize to a plurality of the biomarkers set forth in Table 1D. In varying embodiments, the solid supports comprise a plurality of oligonucleotide probes that hybridize to a plurality of the biomarkers set forth in Table 1A, Table 1B, Table 1C and/or Table 1D. In varying embodiments, the solid support is a microarray. In varying embodiments, the microarray is suitable or configured for use in a microfluidic device. In varying embodiments, the solid supports further comprise a plurality of oligonucleotide probes that hybridize to a plurality of the biomarkers set forth in Table 1E. In varying embodiments, the solid supports further comprise a plurality of oligonucleotide probes that hybridize to a plurality of the biomarkers for diagnosing one or more of cardioembolic stroke, atherothrombotic stroke, carotid stenosis, atrial fibrillation, lacunar stroke, transient ischemic attack, transient neurological events, and hemorrhagic transformation. In varying embodiments, plurality refers to at least 15 biomarkers, e.g., at least 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100 biomarkers, or all listed biomarkers in the identified Table (e.g., Table 1A, Table 1B, Table 1C, Table 1D and/or Table 1E).

In another aspect, provided are reaction mixtures for amplifying one or more exons of a plurality (e.g., 2, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100 biomarkers, or all listed biomarkers in the identified Table, e.g., Table 1A, Table 1B, Table 1C, Table 1D and/or Table 1E) of biomarkers listed in Tables1A-E. In varying embodiments, the reaction mixture comprises one or more primer pairs or a set of primers for amplifying one or more exons of a plurality of the biomarkers set forth in Table 1A. In varying embodiments, the reaction mixture comprises one or more primer pairs or a set of primers for amplifying one or more exons of a plurality of the biomarkers set forth in Table 1B. In varying embodiments, the reaction mixture comprises one or more primer pairs or a set of primers for amplifying one or more exons of a plurality of the biomarkers set forth in Table 1C. In varying embodiments, the reaction mixture comprises one or more primer pairs or a set of primers for amplifying one or more exons of a plurality of the biomarkers set forth in Table 1D. In varying embodiments, the reaction mixture comprises one or more primer pairs or a set of primers for amplifying one or more exons of a plurality of the biomarkers set forth in Table 1A, Table 1B, Table 1C and Table 1D. In varying embodiments, the reaction mixture further comprises one or more primer pairs or a set of primers for amplifying one or more exons of a plurality of the biomarkers set forth in Table 1E. Further provided is a kit comprising the reaction mixtures, as described above and herein.

In a related aspect, provided are kits. In varying embodiments, the kits comprise one or more solid supports, as described herein. In varying embodiments, the kits comprise one or more primer pairs or a set of primers for amplifying one or more exons of a plurality of the biomarkers set forth in Table 1A. In varying embodiments, the kits comprise one or more primer pairs or a set of primers for amplifying one or more exons of a plurality of the biomarkers set forth in Table 1B. In varying embodiments, the kits comprise one or more primer pairs or a set of primers for amplifying one or more exons of a plurality of the biomarkers set forth in Table 1C. In varying embodiments, the kits comprise one or more primer pairs or a set of primers for amplifying one or more exons of a plurality of the biomarkers set forth in Table 1D. In varying embodiments, the kits comprise one or more primer pairs or a set of primers for amplifying one or more exons of a plurality of the biomarkers set forth in Table 1A, Table 1B, Table 1C and Table 1D. In varying embodiments, the kits further comprising a set of primers for amplifying one or more exons of a plurality of the biomarkers set forth in Table 1E.

Definitions

Unless defined otherwise, all technical and scientific terms used herein generally have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Generally, the nomenclature used herein and the laboratory procedures in cell culture, molecular genetics, organic chemistry and nucleic acid chemistry and hybridization described below are those well-known and commonly employed in the art. Standard techniques are used for nucleic acid and peptide synthesis. Generally, enzymatic reactions and purification steps are performed according to the manufacturer's specifications. The techniques and procedures are generally performed according to conventional methods in the art and various general references (see generally, Green and Sambrook, MOLECULAR CLONING: A LABORATORY MANUAL, 4th ed. (2012) Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. and Ausubel, et al., CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, 1987-2015, Wiley Interscience; Wiley Online Library at http://onlinelibrary.wiley.com/book/10.1002/0471142727/homepage/archive.htm), which are provided throughout this document. The nomenclature used herein and the laboratory procedures in analytical chemistry and organic synthesis described below are those well-known and commonly employed in the art. Standard techniques, or modifications thereof, are used for chemical syntheses and chemical analyses.

“Ischemia” or “ischemic event” as used herein refers to diseases and disorders characterized by inadequate blood supply (i.e., circulation) to a local area due to blockage of the blood vessels to the area. Ischemia includes for example, strokes and transient ischemic attacks. Strokes include, e.g., ischemic stroke (including, but not limited to, cardioembolic strokes, atheroembolic or atherothrombotic strokes, i.e., strokes caused by atherosclerosis in the carotid, aorta, heart, and brain, small vessel strokes (i.e., lacunar strokes), strokes caused by diseases of the vessel wall, i.e., vasculitis, strokes caused by infection, strokes caused by hematological disorders, strokes caused by migraines, and strokes caused by medications such as hormone therapy).

The term “transient ischemic attack,” “TIA,” or “mini-stroke” interchangeably refer to a change in the blood supply to a particular area of the brain, resulting in brief neurologic dysfunction that persists, by definition, for less than 24 hours. By definition, a TIA resolves within 24 hours, but most TIA symptoms resolve within a few minutes. If symptoms persist longer, then it is categorized as a stroke. Symptoms include temporary loss of vision (typically amaurosis fugax); difficulty speaking (aphasia); weakness on one side of the body (hemiparesis); numbness or tingling (paresthesia), usually on one side of the body, and dizziness, lack of coordination or poor balance. The symptoms of a TIA usually last a few seconds to a few minutes and most symptoms disappear within 60 minutes.

Transient neurological attacks (TNA) or transient neurological events (TNE) interchangeably refer to events involving neurological symptoms typically lasting only a few minutes or hours and no more than 24 hours. TIAs are considered focal TNAs; other events—including quickly resolving amnesia, confusion, or dizziness and fainting—are considered nonfocal TNAs.

The term “small deep infarct” or “small deep infarction” or “SDI” interchangeably refer to focal infarction of the brain due to an uncertain cause, including but not limited to, cardioembolic, atheroembolic, atherosclerotic disease of the parent artery or disease of the perforating artery.

The term “lacunar stroke” or “lacune” interchangeably refer to focal infarction of the brain due to perforating branch occlusion from microatheroma or lipohyalinosis. Implicit in this definition of lacunar stroke is that the: 1) infarction is not due to cardioembolic source; 2) infarction is not due to atherosclerotic disease of parent arteries; 3) infarction occurs in regions of the brain supplied by penetrating arteries, e.g., basal ganglia, thalamus, internal capsule, corona radiata or pons; 4) lacunar stroke is oftentimes associated with the presence of hypertension, diabetes or other vascular risk factors; and 5) infarcts tend to be smaller, generally less than 50mm in diameter. When the cause of stroke is uncertain or likely other than perforating artery disease, then the more general term—small deep infarct—is appropriate. See, e.g., Caplan, Stroke (2003) 34(3):653-9; Norrving, Pract Neurol (2008) 8:222-228; Lastilla, Clin Exp Hypertens. (2006) 28(3-4):205-15; and Arboix and Marti-Vilalta, Expert Rev Neurother. (2009) 9(2): 179-96.

The term “intracerebral hemorrhage” and “ICH” interchangeably refer to a type of stroke caused by bleeding within the brain tissue itself. Intracerebral hemorrhage occurs when a diseased blood vessel within the brain bursts, allowing blood to leak inside the brain.

An “ischemic stroke/ICH reference expression profile” refers to the pattern of expression of a set of gene exons or splice variants or isoforms (e.g., a plurality of the exons /splice variants or isoforms of the biomarkers set forth in Tables 1A, 1B, 1C, 1D and/or 1E differentially expressed (i.e., overexpressed or underexpressed) in an individual who has suffered or is at risk of experiencing ischemia (e.g., transient cerebral ischemia, transient ischemic attacks (TIA), cerebral ischemia, cardioembolic stroke, large vessel stroke, atherothrombotic stroke, lacunar stroke), intracerebral hemorrhage (ICH) relative to the expression in a control (e.g., the expression level in an individual free of an ischemic stroke/ICH event or the expression level of a stably expressed endogenous reference biomarker). A gene exon/splice variant or isoform from Tables 1A, 1B, 1C, 1D and/or 1E that is expressed at a level that is at least about 1.2-fold, e.g., at least about 1.3-, 1.4-, 1.5-, 1.6-, 1.7-, 1.8-, 1.9-, 2.0-fold, higher than the level in a control is a gene exon/splice variant or isoform overexpressed in ischemic stroke/ICH and a gene exon/splice variant or isoform from Tables 1A, 1B, 1C, 1D and/or 1E that is expressed at a level that is at least about 1.2-fold, e.g., at least about 1.3-, 1.4-, 1.5-, 1.6-, 1.7-, 1.8-, 1.9-, 2.0-fold, lower than the level in a control is a gene isoform underexpressed in ischemic stroke/ICH. Alternately, gene exons/splice variants or isoforms that are expressed at a level that is at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100% higher than the level in a control is a gene exon/splice variant or isoform overexpressed in ischemic stroke/ICH and a gene exon/splice variant or isoform that is expressed at a level that is at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100% lower than the level in a control is a gene exon/splice variant or isoform underexpressed in ischemic stroke/ICH.

A “plurality” refers to two or more, for example, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, 250, 300, 500, 1000, 2000, 5000, or more (e.g., genes). In some embodiments, a plurality refers to concurrent determination of expression levels about 15-85, 20-60 or 40-50 genes, for example, about 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, 250, 300, 500, 1000, 2000, 5000, or more, genes. In some embodiments, “plurality” refers to all genes listed in one or more or all tables, e.g., all genes listed in Tables 1A, 1B, 1C, 1D and/or 1E.

As used herein, the terms “treating” and “treatment” refer to delaying the onset of, retarding or reversing the progress of, reducing the severity of, or alleviating or preventing either the disease or condition to which the term applies, or one or more symptoms of such disease or condition.

The term “mitigating” refers to reduction or elimination of one or more symptoms of that pathology or disease, and/or a reduction in the rate or delay of onset or severity of one or more symptoms of that pathology or disease, and/or the prevention of that pathology or disease. In certain embodiments, the reduction or elimination of one or more symptoms of pathology or disease can include, but is not limited to, reduction or elimination of one or more markers that are characteristic of the pathology or disease.

The terms “subject,” “individual,” and “patient” interchangeably refer to a mammal, preferably a human or a non-human primate, but also domesticated mammals (e.g., canine or feline), laboratory mammals (e.g., mouse, rat, rabbit, hamster, guinea pig) and agricultural mammals (e.g., equine, bovine, porcine, ovine). In various embodiments, the subject can be a human (e.g., adult male, adult female, adolescent male, adolescent female, male child, female child) under the care of a physician or other healthworker in a hospital, psychiatric care facility, as an outpatient, or other clinical context. In certain embodiments the subject may not be under the care or prescription of a physician or other healthworker.

“Sample” or “biological sample” includes sections of tissues such as biopsy and autopsy samples, and frozen sections taken for histologic purposes. Such samples include blood, sputum, tissue, lysed cells, brain biopsy, cultured cells, e.g., primary cultures, explants, and transformed cells, stool, urine, etc. A biological sample is typically obtained from a eukaryotic organism, most preferably a mammal such as a primate, e.g., chimpanzee or human; cow; dog; cat; a rodent, e.g., guinea pig, rat, mouse; rabbit; or a bird; reptile; or fish.

“Array” as used herein refers to a solid support comprising attached nucleic acid or peptide probes. Arrays typically comprise a plurality of different nucleic acid or peptide probes that are coupled to a surface of a substrate in different, known locations.

These arrays, also described as “microarrays” or colloquially “chips” have been generally described in the art, for example, U.S. Pat. Nos. 5,143,854, 5,445,934, 5,744,305, 5,677,195, 6,040,193, 5,424,186 and Fodor et al., Science, 251:767-777 (1991). These arrays may generally be produced using mechanical synthesis methods or light directed synthesis methods which incorporate a combination of photolithographic methods and solid phase synthesis methods. Techniques for the synthesis of these arrays using mechanical synthesis methods are described in, e.g., U.S. Pat. No. 5,384,261. Arrays may comprise a planar surface or may be nucleic acids or peptides on beads, gels, polymeric surfaces, fibers such as fiber optics, glass or any other appropriate substrate as described in, e.g., U .S . Pat. No. 5,770,358, 5,789,162, 5,708,153, 6,040,193 and 5,800,992. Arrays may be packaged in such a manner as to allow for diagnostics or other manipulation of an all-inclusive device, as described in, e.g., U.S. Pat. Nos. 5,856,174 and 5,922,591.

The term “gene” means the segment of DNA involved in producing a polypeptide chain; it includes regions preceding and following the coding region (leader and trailer) as well as intervening sequences (introns) between individual coding segments (exons).

The terms “nucleic acid” and “polynucleotide” are used interchangeably herein to refer to deoxyribonucleotides or ribonucleotides and polymers thereof in either single- or double-stranded form. The term encompasses nucleic acids containing known nucleotide analogs or modified backbone residues or linkages, which are synthetic, naturally occurring, and non-naturally occurring, which have similar binding properties as the reference nucleic acid, and which are metabolized in a manner similar to the reference nucleotides. Examples of such analogs include, without limitation, phosphorothioates, phosphoramidates, methyl phosphonates, chiral-methyl phosphonates, 2-O-methyl ribonucleotides, peptide-nucleic acids (PNAs).

Unless otherwise indicated, a particular nucleic acid sequence also encompasses conservatively modified variants thereof (e.g., degenerate codon substitutions) and complementary sequences, as well as the sequence explicitly indicated. Specifically, degenerate codon substitutions may be achieved by generating sequences in which the third position of one or more selected (or all) codons is substituted with mixed-base and/or deoxyinosine residues (Batzer et al., Nucleic Acid Res. 19:5081 (1991); Ohtsuka et al., J. Biol. Chem. 260:2605-2608 (1985); Rossolini et al., Mol. Cell. Probes 8:91-98 (1994)). The term nucleic acid is used interchangeably with gene, cDNA, mRNA, oligonucleotide, and polynucleotide.

The phrase “stringent hybridization conditions” refers to conditions under which a probe will hybridize to its target subsequence, typically in a complex mixture of nucleic acid, but to no other sequences. Stringent hybridization conditions are sequence-dependent and will be different in different circumstances. Longer sequences hybridize specifically at higher temperatures. An extensive guide to the hybridization of nucleic acids is found in Tijssen, Techniques in Biochemistry and Molecular Biology—Hybridization with Nucleic Probes, “Overview of principles of hybridization and the strategy of nucleic acid assays” (1993). Generally, stringent hybridization conditions are selected to be about 5-10° C. lower than the thermal melting point for the specific sequence at a defined ionic strength Ph. The T_(m) is the temperature (under defined ionic strength, Ph, and nucleic concentration) at which 50% of the probes complementary to the target hybridize to the target sequence at equilibrium (as the target sequences are present in excess, at T_(m), 50% of the probes are occupied at equilibrium). Stringent hybridization conditions will be those in which the salt concentration is less than about 1.0 M sodium ion, typically about 0.01 to 1.0 M sodium ion concentration (or other salts) at Ph 7.0 to 8.3 and the temperature is at least about 30° C. for short probes (e.g., 10 to 50 nucleotides) and at least about 60° C. for long probes (e.g., greater than 50 nucleotides). Stringent hybridization conditions may also be achieved with the addition of destabilizing agents such as formamide. For selective or specific hybridization, a positive signal is at least two times background, optionally 10 times background hybridization. Exemplary stringent hybridization conditions can be as following: 50% formamide, 5×SSC, and 1% SDS, incubating at 42° C., or, 5×SSC, 1% SDS, incubating at 65° C., with wash in 0.2×SSC, and 0.1% SDS at 65° C.

Nucleic acids that do not hybridize to each other under stringent hybridization conditions are still substantially identical if the polypeptides which they encode are substantially identical. This occurs, for example, when a copy of a nucleic acid is created using the maximum codon degeneracy permitted by the genetic code. In such cases, the nucleic acids typically hybridize under moderately stringent hybridization conditions. Exemplary “moderately stringent hybridization conditions” include a hybridization in a buffer of 40% formamide, 1 M NaCl, 1% SDS at 37° C., and a wash in 1×SSC at 45° C. A positive hybridization is at least twice background. Those of ordinary skill will readily recognize that alternative hybridization and wash conditions can be utilized to provide conditions of similar stringency.

The terms “isolated,” “purified,” or “biologically pure” refer to material that is substantially or essentially free from components that normally accompany it as found in its native state. Purity and homogeneity are typically determined using analytical chemistry techniques such as polyacrylamide gel electrophoresis or high performance liquid chromatography. A protein that is the predominant species present in a preparation is substantially purified. The term “purified” denotes that a nucleic acid or protein gives rise to essentially one band in an electrophoretic gel. Particularly, it means that the nucleic acid or protein is at least 85% pure, more preferably at least 95% pure, and most preferably at least 99% pure.

The term “heterologous” when used with reference to portions of a nucleic acid indicates that the nucleic acid comprises two or more subsequences that are not found in the same relationship to each other in nature. For instance, the nucleic acid is typically recombinantly produced, having two or more sequences from unrelated genes arranged to make a new functional nucleic acid, e.g., a promoter from one source and a coding region from another source. Similarly, a heterologous protein indicates that the protein comprises two or more subsequences that are not found in the same relationship to each other in nature (e.g., a fusion protein).

An “expression vector” is a nucleic acid construct, generated recombinantly or synthetically, with a series of specified nucleic acid elements that permit transcription of a particular nucleic acid in a host cell. The expression vector can be part of a plasmid, virus, or nucleic acid fragment. Typically, the expression vector includes a nucleic acid to be transcribed operably linked to a promoter.

The terms “polypeptide,” “peptide” and “protein” are used interchangeably herein to refer to a polymer of amino acid residues. The terms apply to amino acid polymers in which one or more amino acid residue is an artificial chemical mimetic of a corresponding naturally occurring amino acid, as well as to naturally occurring amino acid polymers and non-naturally occurring amino acid polymer.

The term “amino acid” refers to naturally occurring and synthetic amino acids, as well as amino acid analogs and amino acid mimetics that function in a manner similar to the naturally occurring amino acids. Naturally occurring amino acids are those encoded by the genetic code, as well as those amino acids that are later modified, e.g., hydroxyproline, α-carboxyglutamate, and O-phosphoserine. “Amino acid analogs” refers to compounds that have the same basic chemical structure as a naturally occurring amino acid, i.e., an a carbon that is bound to a hydrogen, a carboxyl group, an amino group, and an R group, e.g., homoserine, norleucine, methionine sulfoxide, methionine methyl sulfonium. Such analogs have modified R groups (e.g., norleucine) or modified peptide backbones, but retain the same basic chemical structure as a naturally occurring amino acid. “Amino acid mimetics” refers to chemical compounds that have a structure that is different from the general chemical structure of an amino acid, but that functions in a manner similar to a naturally occurring amino acid.

Amino acids may be referred to herein by either their commonly known three letter symbols or by the one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission. Nucleotides, likewise, may be referred to by their commonly accepted single-letter codes.

“Conservatively modified variants” applies to both amino acid and nucleic acid sequences. With respect to particular nucleic acid sequences, conservatively modified variants refers to those nucleic acids which encode identical or essentially identical amino acid sequences, or where the nucleic acid does not encode an amino acid sequence, to essentially identical sequences. Because of the degeneracy of the genetic code, a large number of functionally identical nucleic acids encode any given protein. For instance, the codons GCA, GCC, GCG and GCU all encode the amino acid alanine. Thus, at every position where an alanine is specified by a codon, the codon can be altered to any of the corresponding codons described without altering the encoded polypeptide. Such nucleic acid variations are “silent variations,” which are one species of conservatively modified variations. Every nucleic acid sequence herein which encodes a polypeptide also describes every possible silent variation of the nucleic acid. One of skill will recognize that each codon in a nucleic acid (except AUG, which is ordinarily the only codon for methionine, and TGG, which is ordinarily the only codon for tryptophan) can be modified to yield a functionally identical molecule. Accordingly, each silent variation of a nucleic acid which encodes a polypeptide is implicit in each described sequence.

As to amino acid sequences, one of skill will recognize that individual substitutions, deletions or additions to a nucleic acid, peptide, polypeptide, or protein sequence which alters, adds or deletes a single amino acid or a small percentage of amino acids in the encoded sequence is a “conservatively modified variant” where the alteration results in the substitution of an amino acid with a chemically similar amino acid.

Conservative substitution tables providing functionally similar amino acids are well known in the art. Such conservatively modified variants are in addition to and do not exclude polymorphic variants, interspecies homologs, and alleles of the invention.

The following eight groups each contain amino acids that are conservative substitutions for one another:

1) Alanine (A), Glycine (G);

2) Aspartic acid (D), Glutamic acid (E);

3) Asparagine (N), Glutamine (Q);

4) Arginine (R), Lysine (K);

5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V);

6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W);

7) Serine (S), Threonine (T); and

8) Cysteine (C), Methionine (M)

(see, e.g., Creighton, Proteins (1984)).

The terms “identical” or percent “identity,” in the context of two or more nucleic acids or polypeptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same (i.e., 60% identity, preferably 65%, 70%, 75%, 80%, 85%, 90%, or 95% identity over a specified region of a ischemic stroke/ICH-associated gene (e.g., a gene set forth in Tables 1A-E), when compared and aligned for maximum correspondence over a comparison window, or designated region as measured using one of the following sequence comparison algorithms or by manual alignment and visual inspection. Such sequences are then said to be “substantially identical.” This definition also refers to the compliment of a test sequence. Preferably, the identity exists over a region that is at least about 25 amino acids or nucleotides in length, or more preferably over a region that is 50-100 amino acids or nucleotides in length.

For sequence comparison, typically one sequence acts as a reference sequence, to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are entered into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. Default program parameters can be used, or alternative parameters can be designated. The sequence comparison algorithm then calculates the percent sequence identities for the test sequences relative to the reference sequence, based on the program parameters. For sequence comparison of nucleic acids and proteins to TIA-associated nucleic acids and proteins, the BLAST and BLAST 2.0 algorithms and the default parameters discussed below are used.

A “comparison window”, as used herein, includes reference to a segment of any one of the number of contiguous positions selected from the group consisting of from 20 to 600, usually about 50 to about 200, more usually about 100 to about 150 in which a sequence may be compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned. Methods of alignment of sequences for comparison are well-known in the art. Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith & Waterman, Adv. Appl. Math. 2:482 (1981), by the homology alignment algorithm of Needleman & Wunsch, J. Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson & Lipman, Proc. Nat'l. Acad. Sci. USA 85:2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.), or by manual alignment and visual inspection (see, e.g., Current Protocols in Molecular Biology (Ausubel et al., eds. 1995 supplement)).

A preferred example of algorithm that is suitable for determining percent sequence identity and sequence similarity are the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al., Nuc. Acids Res. 25:3389-3402 (1977) and Altschul et al., J. Mol. Biol. 215:403-410 (1990), respectively. BLAST and BLAST 2.0 are used, with the parameters described herein, to determine percent sequence identity for the nucleic acids and proteins of the invention. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/). This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul et al., supra). These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always >0) and N (penalty score for mismatching residues; always <0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a word length (W) of 11, an expectation (E) of 10, M=5, N=−4 and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a word length of 3, and expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff & Henikoff, Proc. Natl. Acad. Sci. USA 89:10915 (1989)) alignments (B) of 50, expectation (E) of 10, M=5, N=−4, and a comparison of both strands.

The BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin & Altschul, Proc. Nat'l. Acad. Sci. USA 90:5873-5787 (1993)). One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a nucleic acid is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleic acid to the reference nucleic acid is less than about 0.2, more preferably less than about 0.01, and most preferably less than about 0.001.

An indication that two nucleic acid sequences or polypeptides are substantially identical is that the polypeptide encoded by the first nucleic acid is immunologically cross reactive with the antibodies raised against the polypeptide encoded by the second nucleic acid, as described below. Thus, a polypeptide is typically substantially identical to a second polypeptide, for example, where the two peptides differ only by conservative substitutions. Another indication that two nucleic acid sequences are substantially identical is that the two molecules or their complements hybridize to each other under stringent conditions, as described below. Yet another indication that two nucleic acid sequences are substantially identical is that the same primers can be used to amplify the sequence.

The phrase “selectively (or specifically) hybridizes to” refers to the binding, duplexing, or hybridizing of a molecule only to a particular nucleotide sequence under stringent hybridization conditions when that sequence is present in a complex mixture (e.g., total cellular or library DNA or RNA).

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 illustrates a schematic of alternative splicing. The 3′ and 5′ untranslated regions in mRNA are not depicted.

FIGS. 2A-B illustrates Principal Component Analysis (PCA) (FIG. 2A) and Unsupervised Hierarchical Clustering (FIG. 2B) of 308 exons (292 genes) with differential exon-usage among Intracerebral Hemorrhage, Ischemic Strokes (Cardioembolic, Large Vessel, and Lacunar) and Control. Dendrograms in FIG. 2B are not displayed.

FIG. 3 illustrates Unsupervised Hierarchical Clustering of 308 exons (292 genes) with differential exon- usage among Intracerebral Hemorrhage, Ischemic Strokes (Cardioembolic, Large Vessel, and Lacunar) and Control. Dendrograms are not displayed. This is the same figure as FIG. 2B, with the addition of information on age, time since event, diabetes, hypertension and hyperlipidemia.

DETAILED DESCRIPTION 1. Introduction

Provided are exon or splice variant biomarkers, and methods and tools for using such biomarkers, that can distinguish in a subject suspected of having an ischemic event between no stroke, ischemic stroke (e.g., cardioembolic stroke, large vessel stroke and lacunar stroke) and intracerebral hemorrhage.

2. Subjects Who Can Benefit from the Present Methods

Individuals who will benefit from the present methods may be exhibiting symptoms of or suspected of having experienced a neurological event, ischemic or non-ischemic. In some embodiments, the subject has experienced or is suspected of having experienced an ischemic stroke or ICH. For example, the subject may have suffered, be currently experiencing or suspected of experiencing a small deep infarct (SDI), a transient ischemic attack (TIA), intracerebral hemorrhage (ICH), an ischemic stroke, a myocardial infarction, peripheral vascular disease, or venous thromboembolism. The subject may have or have been diagnosed with cerebral vascular disease or have one or more vascular risk factors (e.g., hypertension, diabetes mellitus, hyperlipidemia, or tobacco smoking).

In some embodiments, the subject has not experienced and/or is not at risk of having an intracerebral hemorrhage. In some embodiments, the subject has not experienced and/or is not at risk of having an intracerebral hemorrhage or hemorrhagic stroke. In some embodiments, the subject has been diagnosed as having not experienced and/or not at risk of having an intracerebral hemorrhage or hemorrhagic stroke.

In some embodiments, the levels of expression of the panel of biomarkers is determined within 3 hours of a suspected ischemic stroke or ICH. In some embodiments, the levels of expression of the panel of biomarkers are determined at 3 or more hours after a suspected ischemic stroke or ICH. In some embodiments, the levels of expression of the panel of biomarkers are determined within 6, 12, 18, 24, 36, 48 hours of a suspected ischemic stroke or ICH.

In some cases, the subject is asymptomatic, but may have a risk or predisposition to experiencing ischemic stroke/ICH, e.g., based on genetics, a related disease condition, environment or lifestyle. For example, in some embodiments, the patient suffers from a chronic inflammatory condition, e.g., has an autoimmune disease (e.g., rheumatoid arthritis, Crohn's disease inflammatory bowel disease), atherosclerosis, hypertension, or diabetes. In some embodiments, the patient has high LDL-cholesterol levels or suffers from a cardiovascular disease (e.g., atherosclerosis, coronary artery disease). In some embodiments, the patient has an endocrine system disorder, a neurodegenerative disorder, a connective tissue disorder, or a skeletal and muscular disorder. Exemplary disorders associated with, related to, or causative of TIA are discussed in co-pending application Ser. No. 13/182,630 and PCT/US2011/044023, which are hereby incorporated herein by reference in their entirety for all purposes. In some embodiments, the subject has an ABCD score that is 4 or greater (see, e.g., Josephson, et al., Stroke. (2008) 39(11):3096-8; Rothwell et al., Lancet (2005) 366(9479):29-36; and Johnston, et al., Lancet. (2007) 369(9558):283-92).

In varying embodiments, the subject may be experiencing or suspected of experiencing a small deep infarct (SDI) or a lacunar stroke. Patients presenting with clinical symptoms of lacunar infarcts or diagnosed as having lacunar syndrome will also benefit from the present diagnostic gene expression profiling. Clinical symptoms of lacunar infarcts include

pure motor hemiparesis

pure sensory stroke

sensorimotor stroke

dysarthria-clumsy hand syndrome

ataxic hemiparesis

Face, arm and leg involvement are characteristic of the first three listed symptoms. A component of ataxia is also present in the last two. Patients with a lacunar syndrome typically have no aphasia, no visuospatial disturbance, no visual field defect, generally no clear disturbance of brainstem function such as pupil abnormalities and eye movement disturbances, and no decreased level of consciousness (as a direct effect rather than as a complication of the stroke) at any time after the stroke. See, Norrving, Pract Neurol (2008) 8:222-228.

3. Biomarkers Indicative of the Occurrence or Risk of Ischemic Stroke/ICH

Biomarkers useful for the prediction, diagnosis or confirmation of the occurrence of ischemic stroke (e.g., a cardioembolic stroke, a large vessel stroke, a lacunar stroke) from an intracerebral hemorrhage (ICH) are listed in Tables 1A-1E. Determination of the gene exon/splice variant or isoform expression levels of a plurality of the biomarkers of Tables 1A-1E can be performed for the prediction, diagnosis or confirmation of the occurrence of ischemic stroke (e.g., a cardioembolic stroke, a large vessel stroke, a lacunar stroke) versus an intracerebral hemorrhage in conjunction with other biomarkers known in the art for the prediction, diagnosis or confirmation of the occurrence of ischemic stroke, in conjunction with other methods known in the art for the diagnosis of ischemic stroke, in conjunction with biomarkers described herein and known in the art useful for determining the cause of ischemic stroke and/or in conjunction with methods known in the art for determining the cause of ischemic stroke. Such biomarkers are described in co-pending and co-owned U.S. Patent Publications Nos. 2015/0018234 (“BIOMARKERS FOR DIAGNOSING ISCHEMIA”); 2012/0316076 (“BIOMARKERS FOR THE DIAGNOSIS OF LACUNAR STROKE”); 2012/0065087 (“BIOMARKERS FOR DIAGNOSIS OF STROKE AND ITS CAUSES”); 2012/0015904 (“BIOMARKERS FOR DIAGNOSIS OF TRANSIENT ISCHEMIC ATTACKS”); and 2010/0197518 (“METHODS FOR DIAGNOSING ISCHEMIA”), each of which is hereby incorporated herein by reference in its entirety for all purposes.

Determination of the expression levels of a plurality of the biomarkers of Tables 1A, 1B, 1C, 1D and/or 1E can be performed for the prediction, diagnosis or confirmation of the occurrence of ischemic stroke/ICH can also be performed independently, e.g., to diagnose whether ischemic stroke and/or ICH has occurred, to distinguish between ischemic stroke and ICH, or to determine the risk that a patient may suffer an ischemic stroke and/or ICH.

As appropriate, the expression levels of at least about 3, 5, 10, 15, 20, 25, 30, 40, 50, 60, 70, 80, 90, 100 or more biomarkers (e.g., gene exons/splice variants or isoforms) from Tables 1A, 1B, 1C, 1D and/or 1E are determined. In some embodiments, the expression levels of a plurality of biomarkers in Tables 1A, 1B, 1C, 1D and/or 1E are determined. In some embodiments, the expression levels of all listed biomarkers in Tables 1A, 1B, 1C, 1D and/or 1E are determined.

In some embodiments, the level of expression of biomarkers indicative of the occurrence of ischemic stroke/ICH is determined within 72 hours, for example, within 60, 48, 36, 24, 12, 6 or 3 hours of a suspected ischemic stroke or ICH.

In various embodiments, an increased expression level of one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, or all, ischemic stroke-associated biomarkers of Table 1A indicates that the subject has or is likely to have experienced, is or is likely to be experiencing cardioembolic ischemic stroke:

TABLE 1A Exon Usage Upregulated in Cardioembolic Ischemic Stroke (CE IS) Marker ID Gene Symbol chr17.73000302-73002235>CDR2L CDR2L chr8.104406853-104407321>shuskeebu shuskeebu chr3.48456585-48456758>PLXNB1 PLXNB1 chr1.86861716-86861980>ODF2L ODF2L chr19.58427747-58427961>ZNF417andZNF814 ZNF417 and ZNF814 chr19.58427747-58427962>ZNF417andZNF814 ZNF417 and ZNF814 chr22.19115606-19115964>skatee Skate chr10.49253461-49254185>BMS1P7 BMS1P7 chr14.70242552-70243107>SLC10A1 SLC10A1 chr7.142630429-142630907>TRPV5 TRPV5 chr10.38299602-38299713>ZNF33A ZNF33A chr10.38299604-38299713>ZNF33A ZNF33A chr2.119988299-119988612>STEAP3 STEAP3 chr2.179463448-179463833>CCDC141andTTN CCDC141 and TTN chr2.25258142-25260100>LOC729723 LOC729723 chr17.34856670-34856801>MYO19 MYO19 chr7.158334118-158334470>PTPRN2 PTPRN2 chr3.188326949-188327341>LPP LPP chr19.18959976-18960257>UPF1 UPF1 chr6.37225553-37225751>TBC1D22B TBC1D22B chr20.43995515-43996066>SYS1-DBNDD2 SYS1-DBNDD2 chr3.49448633-49449168>myforbo myforbo chr4.15570247-15570815>klawgu klawgu

In various embodiments, an increased expression level of one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, or all, ischemic stroke-associated biomarkers of Table 1B indicates that the subject has or is likely to have experienced, is or is likely to be experiencing large vessel or atherothrombotic stroke:

TABLE 1B Exon Usage Upregulated in Large Vessel Ischemic Stroke (LV IS) Marker ID Gene Symbol chr6.37225553-37225751>TBC1D22B TBC1D22B chr20.43995515-43996066>SYS1-DBNDD2 SYS1-DBNDD2 chr3.49448633-49449168>myforbo Myforbo chr4.15570247-15570815>klawgu Klawgu chr14.53248502-53248631>GNPNAT1 GNPNAT1 chr22.29141852-29141991>HSCB HSCB chr16.72146312-72146551>DHX38 DHX38 chr5.176715528-176715928>NSD1 NSD1 chr6.100023529-100023949>RPS3P5 RPS3P5 chr13.103506107-103506224>BIVMandERCC5 BIVM and ERCC5 chr7.2282560-2282685>NUDT1 NUDT1 chr12.54645834-54646013>CBX5 CBX5 chr20.33056659-33057238>vytaw Vytaw chr5.162902464-162902680>HMMR HMMR chr11.62389338-62389650>B3GAT3 B3GAT3 chr15.101847418-101849510>PCSK6 PCSK6 chr5.61688639-61688819>DIMT1L DIMT1L chr12.56334947-56335111>DGKA DGKA chr10.46918169-46918364>FAM35BandRHEBP1 FAM35B and RHEBP1 chr2.20756227-20757430>dawgorbu Dawgorbu chrX.152226503-152227130>PNMA3 PNMA3 chr22.18613610-18614500>PEX26andTUBA8 PEX26 and TUBA8 chr6.111619174-111619775>slyjey Slyjey chr17.43002077-43003869>KIF186 KIF186 chr8.90798887-90799403>RIPK2 RIPK2 chr1.214836934-214837428>CENPF CENPF chr3.8606070-8609807>LMCD1 LMCD1 chr20.52560545-52561537>BCAS1 BCAS1 chr2.173420100-173420449>PDK1 PDK1 chr15.81584265-81585380>IL16 IL16 chr9.131486273-131486411>ZDHHC12 ZDHHC12 chr16.4475881-4476095>DNAJA3 DNAJA3

In various embodiments, an increased expression level of one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, or all, ischemic stroke-associated biomarkers of Table 1C indicates that the subject has or is likely to have experienced, is or is likely to be experiencing lacunar stroke:

TABLE 1C Exon Usage Upregulated in Lacunar IS Marker ID Gene Symbol chr11.119039480-119040013>NLRX1 NLRX1 chr15.52970203-52970321>KIAA1370 KIAA1370 chr11.62475067-62475389>GNG3 GNG3 chr12.94914730-94915696>LOC400061 LOC400061 chr16.15013757-15013942>zoner Zoner chr2.29258330-29258512>FAM179A FAM179A chr18.33077683-33077897>IN080C IN080C chr2.160143094-160143319>WDSUB1 WDSUB1 chr22.44514918-44515022>PARVB PARVB chr5.156821041-156822689>ADAM19 ADAM19 chr6.146285293-146285561>SHPRH SHPRH chr6.146285293-146285527>SHPRH SHPRH chr22.24316496-24316681>GSTTP1andDDT GSTTP1 and DDT chr12.2966630-2968831>FOXM1 FOXM1 chr7.99674926-99675058>ZNF3 ZNF3 chr6.30610545-30612434>C6orf134 C6orf134 chr19.35173682-35173956>ZNF302 ZNF302 chr21.47706315-47706714>C21orf57 C21orf57 chr12.111065735-111066031>TCTN1 TCTN1 chrX.40495835-40495966>CXorf38 CXorf38 chr9.46687439-46688199>KGFLP1 KGFLP1 chr2.101627502-101628004>TBC1D8 TBC1D8 chr1.160580214-160580590>SLAMF1 SLAMF1 chr8.10340434-10340743>LOC346702 LOC346702 chr6.168370462-168372590>MLLT4 MLLT4 chr1.155691308-155691473>DAP3 DAP3 chr12.123262038-123262232>CCDC62 CCDC62 chr14.96795821-96795973>ATG2B ATG2B chr20.32079185-32079984>spawvor spawvor chr6.163984476-163984753>QKI QKI chr1.246729640-246730093>CNST CNST

In various embodiments, an increased expression level of one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 50, 75, 100, 125, 150, 175, 200, or all, ICH-associated biomarkers of Table 1D indicates that the subject has or is likely to have experienced, is or is likely to be experiencing intracerebral hemorrhage:

TABLE 1D Exon Usage Upregulated in Intracerebral Hemorrhage (ICH) Marker ID Gene Symbol chr19.44128266-44128396>CADM4 CADM4 chr5.139929370-139930498>APBB3andSRA1 APBB3 and SRA1 chr1.85127881-85128060>SSX21P SSX21P chr22.31733654-31734033>sneypoy sneypoy chr17.40280569-40280820>RAB5C RAB5C chr3.23929058-23929282>UBE2E1 UBE2E1 chr7.149598-152549>kehera kehera chr3.122283274-122283462>DTX3L DTX3L chr14.76107075-76107405>FLVCR2andTTLL5andC14orf179 FLVCR2 and TTLL5 and C14orf179 chr1.235956803-235956914>LYST LYST chr2.198175302-198175505>ANKRD44 ANKRD44 chr22.20093700-20093802>DGCR8 DGCR8 chr1.112991564-112991796>CTTNBP2NL CTTNBP2NL chr1.19470474-19470587>UBR4 UBR4 chr5.134343647-134343831>PCBD2andCATSPER3 PCBD2 and CATSPER3 chr19.49314066-49314180>BCAT2 BCAT2 chr2.118864235-118864481>INSIG2 INSIG2 chr18.48443613-48443880>ME2 ME2 chr22.45254869-45255778>PRR5-ARHGAP8 PRR5-ARHGAP8 chr1.27431807-27432580>SLC9A1 SLC9A1 chr8.133984843-133984988>TG TG chr6.41751200-41751978>PRICKLE4andTOMM6 PRICKLE4 and TOMM6 chr17.57728564-57728679>CLTC CLTC chr3.150280329-150280449>EIF2A EIF2A chr2.242282407-242282510>SEPT2 SEPT2 chr21.40619627-40619760>BRWD1 BRWD1 chr1.26799700-26800020>HMGN2 HMGN2 chr5.140895496-140896577>DIAPH1 DIAPH1 chr5.140895875-140896577>DIAPH1 DIAPH1 chr1.180049625-180049798>CEP350 CEP350 chr1.180049652-180049798>CEP350 CEP350 chr5.70531277-70532283>goychyby goychyby chr13.100543572-100543868>CLYBL CLYBL chr19.36515246-36515536>CLIP3 CLIP3 chr6.144289727-144290117>PLAGL1andHYMAI PLAGL1 and HYMAI chr21.47608408-47608857>klorley klorley chr9.17135038-17135425>CNTLN CNTLN chr1.114499947-114500542>wawleybo wawleybo chr17.18486655-18486839>CCDC1446 CCDC1446 chr4.40800804-40800923>NSUN7 NSUN7 chr3.39162488-39162682>TTC21A TTC21A chr1.161196029-161196396>TOMM40L TOMM40L chr7.45083306-45083699>CCM2 CCM2 chr19.13009896-13010201>SYCE2 SYCE2 chr3.20019802-20020398>RAB5A RAB5A chr6.122792844-122793052>SERINC1 SERINC1 chr2.231663444-231663881>CAB39 CAB39 chr1.145790974-145791172>GPR89A GPR89A chr4.175223190-175223339>KIAA1712 KIAA1712 chr2.182339687-182340017>ITGA4 ITGA4 chr16.18799866-18800442>ARL6IP1andRPS15A ARL6IP1 and RPS15A chr6.3021094-3022354>teyvybo teyvybo chr16.22277711-22277847>EEF2K EEF2K chr11.7479027-7479176>veemee veemee chrX.77303661-77305894>ATP7A ATP7A chr1.78207302-78207435>USP33 USP33 chrX.76776266-76776396>ATRX ATRX chr12.6761437-6761586>ING4 ING4 chr17.77079383-77079674>ENGASE ENGASE chr11.111889680-111893376>DIXDC1 DIXDC1 chr11.111889680-111893312>DIXDC1 DIXDC1 chr4.157731989-157732171>PDGFC PDGFC chr20.18449588-18449707>POLR3F POLR3F chr11.47738539-47739066>FNBP4 FNBP4 chr16.30593851-30595168>syrar syrar chr13.41593364-41593570>ELF1 ELF1 chr22.51221467-51221716>RABL2B RABL2B chr9.33264164-33264495>CHMP5 CHMP5 chr1.154928545-154928782>SHC1andPYGO2andPBXIP1 SHC1 and PYGO2 and PBXIP1 chr19.1953385-1953507>C19orf34 C19orf34 chr2.113175261-113175493>RGPD8 RGPD8 chr1.145509166-145509614>RBM8A.1 RBM8A.1 chr1.89271574-89271702>PKN2 PKN2 chr10.99433338-99433904>DHDPSLandPI4K2A DHDPSL and PI4K2A chr7.74166365-74166899>GTF21 GTF2I chr18.54318248-54318826>TXNL1 TXNL1 chr12.58345541-58345680>XRCC6BP1 XRCC6BP1 chr7.76870183-76870366>CCDC146 CCDC146 chr3.52385978-52386121>DNAH1 DNAH1 chr12.96258857-96259168>SNRPF SNRPF chr1.63269390-63269535>ATG4C ATG4C chr2.172848099-172848601>HAT1 HAT1 chr18.67508480-67516325>DOK6 DOK6 chr8.30948350-30948460>WRN WRN chr2.208446079-208446886>FAM119A FAM119A chr7.5938415-5938552>CCZ1 CCZ1 chr19.44619641-44619997>ZNF225 ZNF225 chr1.243652316-243652444>SDCCAG8 SDCCAG8 chr4.122723829-122723985>EXOSC9 EXOSC9 chr4.122723829-122723950>EXOSC9 EXOSC9 chr1.46805848-46806593>NSUN4andFAAH NSUN4 and FAAH chr10.51592090-51592621>LOC100287554 LOC100287554 chrX.138864706-138864889>ATP11C ATP11C chr14.50246313-50246526>KLHDC2 KLHDC2 chr7.22980878-22987336>FAM126A FAM126A chr1.150778337-150778494>CTSK CTSK chr12.48094974-48095389>RPAP3 RPAP3 chr15.38619054-38620018>koyzawbu koyzawbu chr11.836251-836527>CD151 CD151 chr17.27581220-27581515>CRYBA1 CRYBA1 chr14.105236090-105236709>AKT1 AKT1 chr10.69828759-69829526>HERC4 HERC4 chr22.50320903-50321183>CRELD2 CRELD2 chr12.10561988-10562185>KLRC4andKLRK1 KLRC4 and KLRK1 chr8.104455023-104455430>DCAF13 DCAF13 chr12.40441853-40442014>SLC2A13 SLC2A13 chrX.16870674-16871151>RBBP7 RBBP7 chr12.54789679-54790162>ITGA5 ITGA5 chr1.150939858-150940192>LASS2 LASS2 chr13.113864293-113864814>PCID2 PCID2 chr15.80191177-80191469>ST20andMTHFS ST20 and MTHFS chr5.145493406-145493876>LARS LARS chr16.3493611-3493839>ZNF174andNAT15andCLUAP1 ZNF174 and NAT15 and CLUAP1 chr6.79664949-79665571>PHIPandTRNAF13P PHIP and TRNAF13P chr17.62745780-62746128>LOC146880 LOC146880 chr17.61473104-61473291>TANC2 TANC2 chr15.59102429-59102589>FAM63B FAM63B chr10.11272033-11272458>CELF2 CELF2 chr20.34487292-34487563>PHF20 PHF20 chr8.74858684-74859057>TCEB1 TCEB1 chr2.17953901-17954053>GEN1 GEN1 chr14.88431849-88431975>GALC GALC chr19.1877203-1877426>FAM108A1 FAM108A1 chr17.18087711-18088069>jeeroy jeeroy chr1.168262382-168262518>SFT2D2andTBX19 SFT2D2 and TBX19 chr6.158088239-158089559>fyjaw fyjaw chr15.30711214-30711350>rukaru rukaru chr8.24256387-24256555>ADAMDEC1 ADAMDEC1 chr15.57545460-57545668>stoyguby stoyguby chr10.75230828-75230969>PPP3CB PPP3CB chr20.43808628-43808777>rotora rotora chr1.46467098-46468409>MAST2 MAST2 chr7.2635311-2636064>dochuby dochuby chr19.11411543-11411914>tojaw tojaw chrX.153744234-153744568>FAM3A FAM3A chr2.73957016-73957158>TPRKB TPRKB chr2.234112772-234113221>INPP5D INPP5D chr6.41036580-41036694>C6orf130andUNC5CL C6orf130 and UNC5CL chr15.75165540-75165690>SCAMP2 SCAMP2 chrX.74282163-74282419>ABCB7 ABCB7 chr2.88336462-88336572>KRCC1 KRCC1 chrX.2839944-2840067>ARSD ARSD chr11.89933252-89935721>CHORDC1 CHORDC1 chr8.62438536-62438673>ASPH ASPH chr3.69028819-69028940>C3orf64 C3orf64 chr5.35053745-35054336>fugey Fugey chr9.35737655-35737938>GBA2 GBA2 chr15.94774950-94775236>MCTP2 MCTP2 chr3.52561845-52561949>NT5DC2 NT5DC2 chr1.85039599-85040105>CTBSandGNG5 CTBS and GNG5 chr10.99195666-99196310>EXOSC1 EXOSC1 chr20.23401942-23402099>NAPB NAPB chr17.36351796-36351998>TBC1D3 TBC1D3 chrX.118985730-118985838>UPF3B UPF3B chr15.66811217-66811418>ZWILCH ZWILCH chr15.66811217-66811469>ZWILCH ZWILCH chr11.125490667-125490903>STT3AandCHEK1 STT3A and CHEK1 chr3.15778540-15778742>ANKRD28 ANKRD28 chr19.9720432-9722014>ZNF562andZNF561 ZNF562 and ZNF561 chr3.167452594-167452719>PDCD10 PDCD10 chr1.10509776-10510381>APITD1andCORT APITD1 and CORT chr6.34360041-34360262>RPS10andNUDT3 RPS10 and NUDT3 chr19.52207575-52207735>NCRNA00085 NCRNA00085 chr11.62105383-62105786>saroro Saroro chr1.17056-17744>WASH7P WASH7P chr1.45987501-45987611>PRDX1 PRDX1 chr1.243419358-243419544>SDCCAG8 SDCCAG8 chr2.111302237-111302385>RGPD6 RGPD6 chr2.110584278-110584426>RGPD5 RGPD5 chr6.109248281-109249438>ARMC2 ARMC2 chr14.96997812-96999042>PAPOLA PAPOLA chr19.58423428-58423556>ZNF417andZNF814 ZNF417 and ZNF814 chr19.58423428-58423559>ZNF417andZNF814 ZNF417 and ZNF814 chrX.149924161-149924398>MTMR1 MTMR1 chr19.5208248-5208404>PTPRS PTPRS chr14.20872770-20872933>TEP1 TEP1 chr20.416929-419487>TBC1D20 TBC1D20 chr15.59943710-59944527>GTF2A2 GTF2A2 chrX.15862547-15863641>AP1S2 AP1S2 chr15.64017491-64017714>HERC1 HERC1 chr5.77656415-77656554>SCAMP1 SCAMP1 chr19.47646729-47646864>SAE1 SAE1 chr19.47646751-47646864>SAE1 SAE1 chr3.81552424-81552867>chordybo chordybo chr1.201780731-201780887>NAV1 NAV1 chr11.61129205-61129722>CYBASC3 CYBASC3 chr11.6523983-6524158>FXC1andDNHD1 FXC1 and DNHD1 chr19.8441789-8441953>lyta Lyta chr6.153291674-153292551>FBXO5 FBXO5 chr6.153291660-153292551>FBXO5 FBXO5 chr6.153291654-153292551>FBXO5 FBXO5 chr7.29549802-29552167>klerky Klerky chr22.41175013-41175131>SLC25A17 SLC25A17 chr4.76874494-76874940>sporsmorby sporsmorby chr5.39274505-39274632>FYB FYB chr10.32324818-32324924>KIF5B KIF5B chr14.52957557-52957725>TXNDC16 TXNDC16 chr14.88452833-88452948>GALC GALC chr20.30720816-30720931>TM9SF4 TM9SF4 chr19.54610118-54610268>NDUFA3 NDUFA3 chr10.92500578-92502287>HTR7 HTR7 chr3.25637911-25639425>RARB RARB chr5.14381239-14381363>TRIO TRIO chr2.243168539-243168821>samemo samemo chr3.137963865-137964525>vusmyby vusmyby chr3.137963930-137964525>ARMC8 ARMC8 chr3.137963930-137964526>ARMC8 ARMC8 chr14.100743755-100744115>YY1 YY1

In varying embodiments, the increased expression level of the gene exon or isoform is at least about 1.2-, e.g., at least about 1.3-, 1.4-, 1.5-, 1.6-, 1.7-, 1.8-, 1.9-, 2.0-fold higher than the expression level in a control.

The overexpression or the underexpression of the biomarkers are determined with reference to a control level of expression. The control level of expression can be determined using any method known in the art. For example, the control level of expression can be from a population of individuals known to not have or be at risk for ischemic stroke or ICH or can be determined with reference to a panel of stably expressed reference biomarkers. Also, threshold levels of expression can be determined based on levels of expression in predetermined populations (e.g., known to not have or be at risk for an ischemic stroke or ICH versus known to have or be at risk for ischemic stroke/ICH). Overexpression or underexpression of a plurality of biomarkers from Tables 1A, 1B, 1C and/or 1D that is at least about 1.2-fold, e.g., at least about 1.3-fold, 1.4-fold, 1.5-fold, 1.6-fold, 1.7-fold, 1.8-fold, 1.9-fold, 2.0-fold, or more, in comparison to the expression levels of a plurality of stably expressed endogenous reference biomarkers, e.g., as described herein or known in the art, is correlative with or indicates that the subject has experienced or is at risk of experiencing an ischemic stroke/ICH. Overexpression or underexpression of a plurality of biomarkers from Tables 1A, 1B, 1C and/or 1D that is at least about 1.2-fold, e.g., 1.3-fold, 1.4-fold, 1.5-fold, 1.6-fold, 1.7-fold, 1.8-fold, 1.9-fold, 2.0-fold, or more, in comparison to the expression level of the same biomarker in an individual or a population of individuals who have not experienced a vascular event is correlative with or indicates that the subject has experienced or is at risk of experiencing an ischemic stroke/ICH.

Biomarkers useful for the determination and diagnosis of the cause of stroke are described, e.g., in co-owned and co-pending U.S. Patent Publications Nos. 2015/0018234 (“BIOMARKERS FOR DIAGNOSING ISCHEMIA”); 2012/0316076 (“BIOMARKERS FOR THE DIAGNOSIS OF LACUNAR STROKE”); 2012/0065087 (“BIOMARKERS FOR DIAGNOSIS OF STROKE AND ITS CAUSES”); 2012/0015904 (“BIOMARKERS FOR DIAGNOSIS OF TRANSIENT ISCHEMIC ATTACKS”); and 2010/0197518 (“METHODS FOR DIAGNOSING ISCHEMIA”), each of which is hereby incorporated herein by reference in its entirety for all purposes. In addition to evaluating the expression levels of a plurality of ischemic stroke/ICH biomarkers of differential gene exon/splice variant/isoform usages, the expression levels of a plurality of biomarkers can be measured to determine whether a suspected or predicted ischemic stroke is cardioembolic, atherosclerotic or lacunar. Furthermore, the expression levels of a plurality of biomarkers can be measured to determine if the cause of stroke is due to carotid stenosis, atrial fibrillation, lacunar stroke or transient ischemic attacks. Classification of stroke subtypes is known in the art and reviewed in, e.g., in Amarenco, et al., Cerebrovasc Dis (2009) 27:493-501. Accordingly, in some embodiments, the expression levels of at least about 3, 5, 10, 15, 20, 25, 30, 40, 50, 60, 70, 80, 85, 100, 200, 500, 1000 or more, ischemic stroke-associated biomarkers are independently determined. In some embodiments, the expression levels of all ischemic stroke-associated biomarkers in a panel are determined.

In various embodiments, the expression levels of a plurality of ischemic stroke-associated exon/splice variant biomarkers are co-determined together with the expression levels of a plurality of genes useful in the determination of whether a patient has experienced or has a predisposition to experience cardioembolic stroke (a.k.a., cardiac embolism, cardioembolism emboligenic heart disease). A cardioembolic stroke occurs when a thrombus (clot) dislodges from the heart, travels through the cardiovascular system and lodges in the brain, first cutting off the blood supply and then often causing a hemorrhagic bleed. In some embodiments an increased expression level of one or more ischemic stroke-associated biomarkers selected from the group consisting of IRF6 (NM_006147), ZNF254 (NM_203282), GRM5 (NM_000842 /// NM_001143831), EXT2 (NM_000401 /// NM_207122), AP3S2 (NM_005829 /// NR_023361), PIK3C2B (NM_002646), ARHGEFS (NM_005435), COL13A1 (NM_001130103 /// NM_005203 /// NM_080798 /// NM_080799 /// NM_080800 /// NM_080801 /// NM_080802 /// NM_080803 /// NM_080804 /// NM_080805 /// NM_080806 /// NM_080807 /// NM_080808 /// NM_080809 /// NM_080810 /// NM_080811 /// NM_080812 /// NM_080813 /// NM_080814 /// NM_080815), PTPN20A /// PTPN2OB (NM_001042357 /// NM_001042358 /// NM_001042359 /// NM_001042360 /// NM_001042361 /// NM_001042362 /// NM_001042363 /// NM_001042364 /// NM_001042365 /// NM_001042387 /// NM_001042389 /// NM_001042390 /// NM_001042391 /// NM_001042392 /// NM_001042393 /// NM_001042394 /// NM_001042395 /// NM_001042396 /// NM_001042397 /// NM_015605), LHFP (NM_005780), BANK1 (NM_001083907 /// NM_001127507 /// NM_017935), HLA-DOA (NM_002119), EBF1 (NM_024007), TMEM19 (NM_018279), LHFP (NM_005780), FCRL1 (NM_001159397 /// NM_001159398 /// NM_052938), OOEP (NM_001080507) and LRRC37A3 (NM_199340) is correlative with or indicates that the patient has experienced or is at risk for cardioembolic stroke. In some embodiments, a decreased expression level of one or more ischemic stroke-associated biomarkers selected from the group consisting of LOC284751 (NM_001025463), CD46 (NM_002389 /// NM_153826 /// NM_172350 /// NM_(—)172351 /// NM_172352 /// NM_172353 /// NM_172354 /// NM_172355 /// NM_172356 /// NM_172357 /// NM_172358 /// NM_172359 /// NM_172360 /// NM_172361), ENPP2 (NM_001040092 /// NM_001130863 /// NM_006209), C19orf28 (NM_001042680 /// NM_021731 /// NM_174983), TSKS (NM_021733), CHURC1 (NM_145165), ADAMTSL4 (NM_019032 /// NM_025008), FLJ40125 (NM_001080401), CLEC18A (NM_001136214 /// NM_182619), ARHGEF12 (NM_015313), C16orf68 (NM_024109), TFDP1 (NM_007111 /// NR_026580) and GSTK1 (NM_001143679 /// NM_001143680 /// NM_001143681 /// NM_015917) is correlative with or indicates that the patient has experienced or is at risk for cardioembolic stroke.

In various embodiments, the expression levels of a plurality of ischemic stroke-associated exon/splice variant biomarkers are co-determined together with the expression levels of a plurality of genes useful in the determination of whether a patient has experienced or has a predisposition to experience carotid stenosis. Carotid stenosis is a narrowing or constriction of the inner surface (lumen) of the carotid artery, usually caused by atherosclerosis. An inflammatory buildup of plaque can narrow the carotid artery and can be a source of embolization. Emboli break off from the plaque and travel through the circulation to blood vessels in the brain, causing ischemia that can either be temporary (e.g., a transient ischemic attack), or permanent resulting in a thromboembolic stroke (a.k.a., atherothrombosis, large-artery atherosclerosis, atherosclerosis with stenosis). In some embodiments, an increased expression level of one or more ischemic stroke-associated biomarkers selected from the group consisting of NTSE (NM_002526), CLASP2 (NM_015097), GRM5 (NM_000842 /// NM_001143831), PROCR (NM_006404), ARHGEFS (NM_005435), AKR1C3 (NM_003739), COL13A1 (NM_001130103 /// NM_005203 /// NM_080798 /// NM_080799 /// NM_080800 /// NM_080801 /// NM_080802 /// NM_080803 /// NM_080804 /// NM_080805 /// NM_080806 /// NM_080807 /// NM_080808 /// NM_080809 /// NM_080810 /// NM_080811 /// NM_080812 /// NM_080813 /// NM_080814 /// NM_080815), LHFP (NM_005780), RNF7 (NM_014245 /// NM_183237), CYTH3 (NM_004227), EBF1 (NM_024007), RANBP10 (NM_020850), PRSS35 (NM_153362), C12orf42 (NM_001099336 /// NM_198521) and LOC100127980 (XM_001720119 /// XM_001722650) is correlative with or indicates that the patient has experienced or is at risk for carotid stenosis. In some embodiments, a decreased expression level of one or more ischemic stroke-associated biomarkers selected from the group consisting of FLJ31945 (XM_001714983 /// XM_(—)001716811 /// XM_001718431), LOC284751 (NM_001025463), LOC100271832 (NR_027097), MTBP (NM_022045), ICAM4 (NM_001039132 /// NM_001544 /// NM022377), SHOX2 (NM_001163678 /// NM_003030 /// NM_006884), DOPEY2 (NM_005128), CMBL (NM_138809), LOC146880 (NR_026899 /// NR_027487), SLC20A1 (NM_005415), SLC6A19 (NM_001003841), ARHGEF12 (NM_015313), C16orf68 (NM_024109), GIPC2 (NM_017655) and LOC100144603 (NR_021492) is correlative with or indicates that the patient has experienced or is at risk for carotid stenosis.

In various embodiments, the expression levels of a plurality of ischemic stroke-associated exon/splice variant biomarkers are co-determined together with the expression levels of a plurality of genes useful in the determination of whether a patient has experienced or has a predisposition to experience atrial fibrillation. Atrial fibrillation (AF or A-fib) is the most common cardiac arrhythmia and involves the two upper chambers (atria) of the heart fibrillating (i.e., quivering) instead of a coordinated contraction. In some instances, cardioembolic stroke can occur as a result of atrial fibrillation. Cardioembolic stroke can be a downstream result of atrial fibrillation in that stagnant blood in the fibrillating atrium can form a thrombus that then embolises to the cerebral circulation, blocking arterial blood flow and causing ischaemic injury. In some embodiments, an increased expression level of one or more ischemic stroke-associated biomarkers selected from the group consisting of SMC1A (NM_006306), SNORA68 (NR_000012), GRLF1 (NM_004491), SDC4 (NM_002999), HIPK2 (NM_001113239 /// NM_022740 /// XM_001716827 /// XM 925800), LOC100129034 (NR_027406 /// XR 079577), CMTM1 (NM_052999 /// NM_181268 /// NM_181269 /// NM_181270 /// NM_181271 /// NM_181272 /// NM_181283 /// NM_181296) and TTC7A (NM_020458) is correlative with or indicates that the patient has experienced or is at risk for atrial fibrillation. In some embodiments, a decreased expression level of one or more ischemic stroke-associated biomarkers selected from the group consisting of LRRC43 (NM_001098519 /// NM_152759), MIF /// SLC2A11 (NM_001024938 /// NM_001024939 /// NM_002415 /// NM_030807), PER3 (NM_016831), PPIE (NM_006112 /// NM_203456 /// NM_203457), COL13A1 (NM_001130103 /// NM_005203 /// NM_080798 /// NM_080799 /// NM_080800 /// NM_080801 /// NM_080802 /// NM_080803 /// NM_080804 /// NM_080805 /// NM_080806 /// NM_080807 /// NM_080808 /// NM_080809 /// NM_080810 /// NM_080811 /// NM_080812 /// NM_080813 /// NM_080814 /// NM_080815), DUSP16 (NM_030640), BRUNOL6 (NM_052840), GPR176 (NM_007223), C6orf164 (NR_026784) and MAP3K7IP1 (NM_006116 /// NM_153497) is correlative with or indicates that the patient has experienced or is at risk for atrial fibrillation.

In various embodiments, the expression levels of a plurality of ischemic stroke-associated exon/splice variant biomarkers are co-determined together with the expression levels of a plurality of genes useful in the determination of whether a patient has experienced or has a predisposition to experience transient ischemic attacks (TIA). A transient ischemic attack is a change in the blood supply to a particular area of the brain, resulting in brief neurologic dysfunction that persists, by definition, for less than 24 hours. If symptoms persist longer, then it is categorized as a stroke. In some embodiments, an increased expression level of one or more TIA-associated biomarkers selected from the group consisting of GABRB2 (NM_000813 /// NM_021911), ELAVL3 (NM_001420 /// NM_032281), COL1A1 (NM_000088), SHOX2 (NM_003030 /// NM_006884), TWIST1 (NM_000474), DPPA4 (NM_018189), DKFZP434P211 (NR_003714), WIT1 (NM_015855 /// NR_023920), SOX9 (NM_000346), DLX6 (NM_005222), ANXA3 (NM_005139), EPHA3 (NM_005233 /// NM_182644), SOX11 (NM_003108), SLC26A8 (NM_052961 /// NM_138718), CCRL1 (NM_016557 /// NM_178445), FREM2 (NM_207361), STOX2 (NM_020225), ZNF479 (NM_033273 /// XM_001714591 /// XM_001719979), LOC338862 (NR_038878.1), ASTN2 (NM_014010 /// NM_198186 /// NM_198187 /// NM_198188), FOLH1 (NM_001014986 /// NM_004476), SNX31 (NM_152628), KREMEN1 (NM_001039570 /// NM_001039571), ALS2CR11 (NM_152525), FIGN (NM_018086), RORB (NM_006914), LOC732096 (XM_001720784 /// XM_001725388 /// XR 016064), GYPA (NM_002099), ALPL (NM_000478 /// NM_001127501), LHX2 (NM_004789), GALNTS (NM_014568), SRD5A2L2 (NM_001010874), GALNT14 (NM_024572), OVOL2 (NM_021220), BMPR1B (NM_001203), UNCSB (NM_170744), ODZ2 (NM_001080428 /// NM_001122679), RASAL2 (NM_004841 /// NM_170692), SHOX (NM_000451 /// NM_006883), C19orf59 (NM_174918), ZNF114 (NM_153608), SRGAP1 (NM_020762), ELAVL2 (NM_004432), NCRNA00032 (XM 376821 /// XM 938938), LOC440345 (XR 015786), FLJ30375 (XM_001724993 /// XM_001725199 /// XM_001725628), TFPI (NM_001032281 /// NM_006287), PTGR1 (NM_012212), ROBO1 (NM_002941 /// NM_133631), NR2F2 (NM_021005), GRMS (NM_000842 /// NM_001143831), LUM (NM_002345), FLJ39051 (NR_033839.1), COL1A2 (NM_000089), CASP5 (NM_001136109 /// N1V1 001136110 /// N1V1 001136111 /// N1V1 001136112 /// NM_004347 //), OPCML (NM_001012393 /// NM_002545), TTC6 (NM_001007795), TFAP2B (NM_003221), CRISP2 (NM_001142407 /// NM_001142408 /// NM_001142417 /// NM_001142435 /// NM_003296), SOX11 (NM_003108), ANKRD30B (XM_001716904 /// XM_001717561 /// XM_001717810), SCN2A (NM_001040142 /// NM_001040143 /// NM_021007), MYNN (NM_018657), FOXA2 (NM_021784 /// NM_153675), DKFZP434B061 (XR 015528 /// XR 040812), LOC645323 (NR_015436 /// NR_024383 /// NR_024384 /// XR 041118 /// XR 041119 /// XR 041120), SNIP (NM_025248), LOC374491 (NR_002815), ADAM30 (NM_021794), SIX3 (NM_005413), FLJ36144 (XR 040632 /// XR 040633 /// XR 040634), CARD8 (NM_014959), RP1-127L4.6 (NM_001010859), FAM149A (NM_001006655 /// NM_015398), B3GAT2 (NM_080742), SPOCK3 (NM_001040159 /// NM_016950), ITGBL1 (NM_004791), IQGAP3 (NM_178229), C7orf45 (NM_145268), ZNF608 (NM_020747), LOC375010 (XR 041271), LRP2 (NM_004525), TGFB2 (NM_001135599 /// NM_003238), SHOX2 (NM_003030 /// NM_006884), HOXC4 /// HOXC6 (NM_004503 /// NM_014620 /// NM_153633 /// NM_153693), ELTD1 (NM_022159), FAM182B /// RP13-401N8.2 (XM_001132551 /// XM_001133521 /// XM_001718365 /// XM 933752), LIFR (NM_001127671 /// NM_002310), FOLH1 (NM_001014986 /// NM_004476), EHF (NM_012153), NDST3 (NM_004784), BRUNOLS (NM_021938), LOC728460 (XM_001128581 /// XM_001129498 /// XM_001723364), PDE1A (NM_001003683 /// NM_005019), POU2AF1 (NM_006235), FAT1 (NM_005245), PCDH11X /// PCDH11Y (NM_014522 /// NM_032967 /// NM_032968 /// NM_032969 /// NM_032971 /// NM_032972), FLJ37786 (XR 041472 /// XR 041473), SLC22A4 (NM_003059), DHRS13 (NM_144683), MEG3 (NR_002766 /// NR_003530 /// NR_003531), PIWIL1 (NM_004764), LOC203274 (AL117607.1 /// BC080605.1), LOC100133920 /// LOC286297 /// (NR_024443 /// XM_001714612 /// XM 372109 /// XM 933054 /// XM_933058), DMRT1 (NM_021951), ADM (NM_001124), VWA3B (NM_144992), GAFA3 (XM_001715321 /// XM_001722922 /// XM_001723636), HESX1 (NM_003865), ADAMDEC1 (NM_014479), CAV1 (NM_001753), LAMB4 (NM_007356), TPTE (NM_199259 /// NM_199260 /// NM_199261), PPP1R1C (NM_001080545), HPSE (NM_001098540 /// NM_006665), AIM2 (NM_004833), RUNDC3B (NM_001134405 /// NM_001134406 /// NM_138290), CARD16 (NM_001017534 /// NM_052889), FAM124A (NM_145019), MGC39584 (XR 017735 /// XR 017787 /// XR 041937), OSM (NM_020530), RFX2 (NM_000635 /// NM_134433), MYBPC1 (NM_002465 /// NM_(—)206819 /// NM_206820 /// NM_206821), LTBR (NM_002342), C18orf2 (NM_031416 /// NR_023925 /// NR_023926 /// NR_023927 /// NR_023928), SNRPN (NM_003097 /// NM_022805 /// NM_022806 /// NM_022807 /// NM_022808 /// NR_001289), FLJ36031 (NM_175884), IL1B (NM_000576), TRPM1 (NM_002420), OSTCL (NM_145303), MAPK14 (NM_001315 /// NM_139012 /// NM_139013 /// NM_139014), KCNJ15 /// LOC100131955 (NM_002243 /// NM_170736 /// NM_170737 /// XM_001713900 /// XM_001715532 /// XM_0), FIGN (NM_018086), HNT (NM_001048209 /// NM_016522), S100Al2 (NM_005621), CHIT1 (NM_003465), C7orf53 (NM_001134468 /// NM_182597), FAM13A1 (NM_001015045 /// NM_014883), GNAO1 (NM_020988 /// NM_138736), MAPK14 (NM_001315 /// NM_139012 /// NM_139013 /// NM_139014), FAM55D (NM_001077639 /// NM_017678), PRKD2 (NM_001079880 /// NM_001079881 /// NM_001079882 /// NM_016457), LIMK2 (NM_001031801 /// NM_005569 /// NM_016733), C18orf54 (NM_173529), IGFBP5 (NM_000599), EVI1 (NM_001105077 /// NM_001105078 /// NM_005241), PLSCR1 (NM_021105), FOXC1 (NM_001453), LOC646627 (NM_001085474), ZNF462 (NM_021224), CNTLN (NM_001114395 /// NM_017738), ZNF438 (NM_001143766 /// NM_001143767 /// NM_001143768 /// NM_001143769 /// NM_001143770), DEFB105A /// DEFB105B (NM_001040703 /// NM_152250), LOC340017 (NR_026992.1), C1orf67 (NM_144989), ACSL1 (NM_001995), ADH1B (NM_000668), SLC2A14 /// SLC2A3 (NM_006931 /// NM_153449), IL1B (NM_000576), ST3GAL4 (NM_006278 /// XM_001714343 /// XM_001726541 /// XM_001726562), UBE2J1 (NM_016021), PNPLA3 (NM_025225) and PAPPA (NM_002581) is correlative with or indicates that the patient has experienced or is at risk for TIA. In some embodiments, a decreased expression level of one or more TIA-associated biomarkers selected from the group consisting of NBPF10 /// RP11-9412.2 (NM_001039703 /// NM_183372 /// XM_001722184), SFXN1 (NM_022754), SPIN3 (NM_001010862), UNC84A (NM_001130965 /// NM_025154), OLFM2 (NM_058164), PPM1K (NM_152542), P2RY10 (NM_014499 /// NM_198333), ZNF512B (NM_020713), MORF4L2 (NM_001142418 /// NM_001142419 /// NM_001142420 /// NM_001142421 /// NM_001142422), GIGYF2 (NM_001103146 /// NM_001103147 /// NM_001103148 /// NM_015575), ERAP2 (NM_001130140 /// NM_022350), SLFN13 (NM_144682), LOC401431 (XR 040272 /// XR 040273 //// XR_040274 /// XR 040275), MED6 (NM_005466), BAIAP2L1 /// LOC100128461 (NM_018842 /// XM_001722656 /// XM_001724217 /// XM_001724858), LNPEP (NM_005575 /// NM_175920), MBNL1 (NM_021038 /// NM_207292 /// NM_207293 /// NM_(—)207294 /// NM_207295 /// NM_207296), NOS3 (NM_000603), MCF2L (NM_001112732 /// NM_024979), KIAA1659 (XM_001723799 /// XM_001725435 /// XM_001726785), SCAMPS (NM_138967), LOC648921 (XM_001715629 /// XM_001720571 /// XR 018520), ANAPC5 (NM_001137559 /// NM_016237), SPON1 (NM_006108), FUS (NM_004960), GPR22 (NM_005295), GAL3ST4 (NM_024637), METTL3 (NM_019852), LOC100131096 (XM_001720907 /// XM_001726205 /// XM_001726705), FAAH2 (NM_174912), SMURF2 (NM_022739), SNRPN (NM_003097 /// NM_022805 /// NM_022806 /// NM_022807 /// NM_022808 /// NR_001289), FBLN7 (NM_001128165 /// NM_153214), GLS (NM_014905), G3BP1 (NM_005754 /// NM198395), RCAN3 (NM_013441), EPHX2 (NM_001979), DIP2C (NM_014974), CCDC141 (NM_173648), CLTC (NM_004859), FOSB (NM_001114171 /// NM006732), CACNA1I (NM_001003406 /// NM_021096), UNQ6228 (XM_001725293 /// XM_001725359 /// XM_001726164), ATG9B (NM_173681), AK5 (NM_012093 /// NM_174858), RBM14 (NM_006328), MAN1C1 (NM_020379), HELLS (NM_018063), EDAR (NM_022336), SLC3A1 (NM_000341), ZNF519 (NM_145287), LOC100130070 /// LOC100130775 /// LOC100131787 /// LOC100131905 /// LOC100132291 /// LOC100132488 /// RPS27 (NM_001030 /// XM_001721002 /// XM_001722161 /// XM_001722965 /// XM_001723889 //), ZC3H12B (NM_001010888), IQGAP2 (NM_006633), SOX8 (NM_014587), WHDC1L2 (XM 926785), TNPO1 (NM_002270 /// NM_153188), TNFRSF21 (NM_014452), TSHZ2 (NM_173485), DMRTC1 /// DMRTC1B (NM_001080851 /// NM_033053), GSTM1 (NM_000561 /// NM_146421), GSTM2 (NM_000848 /// NM_001142368), PNMA6A (NM_032882), CAND1 (NM_018448), CCND3 (NM_001136017 /// NM_001136125 /// NM_001136126 /// NM_001760), GSTM1 (NM_000561 /// NM_146421), and GUSBL2 (NR_003660 /// XR_042150 /// XR 042151) is correlative with or indicates that the patient has experienced or is at risk for TIA. Further biomarkers of interest are published in Zhan, et al., Neurology. (2011) 77(19):1718-24.

In various embodiments, the expression levels of a plurality of ischemic stroke-associated exon/splice variant biomarkers are co-determined together with the expression levels of a plurality of genes useful in the determination of whether a patient has experienced or has a predisposition to experience a transient neurological event (TNE). In some embodiments, an increased expression level of one or more (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or all) ischemic stroke-associated biomarkers selected from the group consisting of UBE2J1, ELAVL3, FCGR2B, BLVRA, JMJD6, DDAH2, PTRH2, CARD16, CAV1, ZNF608, NDUFB3, SLC22A4, PCMT1, CACNA1A, CASP1 and LOC100129105 indicates that the patient has suffered or is at risk of experiencing a transient neurological event (TNE). In some embodiments, an increased expression level of one or more (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 35, 40 or all) ischemic stroke-associated biomarkers selected from the group consisting of AIM2, Cl4orf101, DNAH17, UBE2J1, LOC203274, PGS1, ZEB2, DDAH2, CARD16, SPATA4, ANXA3, WIT1, FCGR2B, CACNA1A, FKBP15, N4BP2L2, HNRNPH2, ELAVL3, ZNF608, TLR10, BLVRA, SLC22A4, RAB27A, LTBR, CARD16 III CASP1, IGFBP5, CASP5, LTB, NDUFB3, SHOX2, CAV1, CNIH4, FLJ39051, CASP1, PTRH2, LOC100129105, PCMT1, CYTH4, JMJD6, DRAM1, FCGR1B indicates that the patient has suffered or is at risk of experiencing a transient neurological event (TNE). In some embodiments, an increased expression level of one or more (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30 or all) ischemic stroke-associated biomarkers selected from the group consisting of CARD16, IRF7, TLR6, NMU, C13orf16, TAPBP, BTC, ZBP1, HSPA6, TWIST1, PLSCR1, SAMD9L, OSTCL, C9orf66, GYPA, ADM, ANKRD22, SHOX, ZNF354A, SRGAP1, GRMS, BAGE, XRCC4, SLC37A3, OVOL2, LIFR, RASAL2, hCG_1749898, IQGAP3, HS3ST3A1, NPR3, SIX3 and HCN1 indicates that the patient has suffered or is at risk of experiencing a transient neurological event (TNE). In some embodiments, an increased expression level of one or more (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 35, 40 or all) ischemic stroke-associated biomarkers selected from the group consisting of UBE2J1, CARD16, LOC203274, ZNF608, CARD16 /// CASP1, PTRH2, ANXA3, FCGR2B, C14orf101, LOC100129105, DDAH2, RAB27A, AIM2, CASP5, HNRNPH2, RAB27A, SHOX2, CNIH4, TLR10, ZEB2, NDUFB3, CYTH4, BLVRA, FLJ39051, SLC22A4, DNAH17, SPATA4, CACNA1A, CASP1, PGS1, LTBR, FCGR1B, IGFBP5, LTB, N4BP2L2, DRAM1, WIT1, ELAVL3, FKBP15, JMJD6, CAV1 and PCMT1 indicates that the patient has suffered or is at risk of experiencing a transient neurological event (TNE). Conversely, in some embodiments, a decreased expression level of one or more (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or all) ischemic stroke-associated biomarkers selected from the group consisting of UBE2J1, ELAVL3, FCGR2B, BLVRA, JMJD6, DDAH2, PTRH2, CARD16, CAV1, ZNF608, NDUFB3, SLC22A4, PCMT1, CACNA1A, CASP1 and LOC100129105 indicates that the patient has not suffered or is not at risk of experiencing a transient neurological event (TNE). In some embodiments, a decreased expression level of one or more (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 35, 40 or all) ischemic stroke-associated biomarkers selected from the group consisting of AIM2, Cl4orf101, DNAH17, UBE2J1, LOC203274, PGS1, ZEB2, DDAH2, CARD16, SPATA4, ANXA3, WIT1, FCGR2B, CACNA1A, FKBP15, N4BP2L2, HNRNPH2, ELAVL3, ZNF608, TLR10, BLVRA, SLC22A4, RAB27A, LTBR, CARD16 /// CASP1, IGFBP5, CASP5, LTB, NDUFB3, SHOX2, CAV1, CNIH4, FLJ39051, CASP1, PTRH2, LOC100129105, PCMT1, CYTH4, JMJD6, DRAM1, FCGR1B indicates that the patient has not suffered or is not at risk of experiencing a transient neurological event (TNE). In some embodiments, a decreased expression level of one or more (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30 or all) ischemic stroke-associated biomarkers selected from the group consisting of CARD16, IRF7, TLR6, NMU, C13orf16, TAPBP, BTC, ZBP1, HSPA6, TWIST1, PLSCR1, SAMD9L, OSTCL, C9orf66, GYPA, ADM, ANKRD22, SHOX, ZNF354A, SRGAP1, GRMS, BAGE, XRCC4, SLC37A3, OVOL2, LIFR, RASAL2, hCG_1749898, IQGAP3, HS3ST3A1, NPR3, SIX3 and HCN1 indicates that the patient has not suffered or is not at risk of experiencing a transient neurological event (TNE). In some embodiments, a decreased expression level of one or more (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 35, 40 or all) ischemic stroke-associated biomarkers selected from the group consisting of UBE2J1, CARD16, LOC203274, ZNF608, CARD16 /// CASP1, UBE2J1, PTRH2, ANXA3, FCGR2B, Cl4orf101, LOC100129105, DDAH2, RAB27A, AIM2, CASP5, HNRNPH2, RAB27A, SHOX2, CNIH4, TLR10, ZEB2, NDUFB3, CYTH4, BLVRA, FLJ39051, SLC22A4, DNAH17, SPATA4, CACNA1A, CASP1, PGS1, LTBR, FCGR1B, IGFBP5, LTB, N4BP2L2, DRAM1, WIT1, ELAVL3, FKBP15, JMJD6, CAV1 and PCMT1 indicates that the patient has not suffered or is not at risk of experiencing a transient neurological event (TNE).

In various embodiments, the expression levels of a plurality of ischemic stroke-associated exon/splice variant biomarkers are co-determined together with the expression levels of a plurality of genes useful in the determination of whether a patient has experienced or has a predisposition to experience lacunar stroke. In some embodiments, an increase of the expression level of one or more biomarkers selected from the group consisting of RASEF (NM_152573), CALM1 (NM_006888), TTC12 (NM_017868), CCL3 /// CCL3L1 /// CCL3L3 (NM_001001437 /// NM_002983 /// NM_021006), CCDC78 (NM_001031737), PRSS23 (NM_007173), LAIR2 (NM_002288 /// NM_021270), C18orf49 (AK000229.1 /// BC047606.1), UTS2 (NM_006786 /// NM_021995), LGR6 (NM_001017403 /// NM_001017404 /// NM_021636), PROCR (NM_006404), LAG3 (NM_002286), OASL (NM_003733 /// NM_198213), LOC100132181 (XM_001722051.1), HLA-DRB4 (NM_021983 /// XM_002346251), CCL2 (NM_002982), ALS2CR11 (NM_152525), SCAND2 (NR_003654 /// NR_004859), GBP4 (NM_052941), RUNX3 (NM_001031680 /// NM_004350), TSEN54 (NM_207346), UBA7 (NM_003335), FAM179A (NM_199280), TGFBR3 (NM_003243), CCDC114 (NM_144577), AKAP9 (NM_005751 /// NM_147185), BNC2 (NM_017637), BZRAP1 (NM_004758 /// NM_024418), CCL4 (NM_002984), CHST2 (NM_004267), CSF1 (NM_000757 /// NM_172210 /// NM_172211 /// NM_172212), ERBB2 (NM_001005862 /// NM_004448), GBR56 (NM_001145770 /// NM_001145771 /// NM_001145772 /// NM_001145773 /// NM_001145774), GRAMD3 (NM_001146319 /// NM_001146320 /// NM_001146321 /// NM_001146322 /// NM_023927), GRHL2 (NM_024915), GRK4 (NM_001004056 /// NM_001004057 /// NM_182982), ITIH4 (NM_002218), KIAA1618 (NM_020954), LOC147646 (XM_001134195 /// XM_001134326 /// XM_001726058), LOC150622 (NR_026832), LOC161527 (NM_002675 /// NM_033238 /// NM_033239 /// NM_033240/// NM_033244 /// NM_033246), PLEKHF1 (NM_024310), PRKD2 (NM_001079880 /// NM_001079881 /// NM_001079882 /// NM_016457), RGNEF (NM_001080479), SESN2 (NM_031459), SLAMF7 (NM_021181), SPON2 (NM_001128325/// NM_012445), STAT1 (NM_007315/// NM_139266), SYNGR1 (NM_004711 /// NM_145731 /// NM_145738), TRX21 (NM_013351), TMEM67 (NM_001142301 /// NM_153704 /// NR_024522), TUBE1 (NM_016262), and ZNF827 (NM_178835), and/or a decrease of the expression level of one or more biomarkers selected from the group consisting of HLA-DQA1 (NM_002122), FLJ13773 (AK023835.1), QKI (NM_006775/// NM_206853/// NM_206854/// NM_206855), MPZL3 (NM_198275), FAM70B (NM_182614), LOC254128 (NR_037856.1 /// NR_037857.1 /// NR_037858.1), IL8 (NM_000584), CHML (NM_001821), STX7 (NM_003569), VAPA (NM_003574 /1/NM_194434), UGCG (NM_003358), PDXDC1 (NM_015027), LRRC8B (NM_001134476/// NM_015350), STK4 (NM_006282), GTF2H2 (NM_001515), AGFG1 (NM_001135187 /// NM_001135188 /// NM_001135189 /// NM_004504), BTG1 (NM_001731), CFDP1 (NM_006324), CNPY2 (NM_014255), FAM105A (NM_019018), GATM (NM_001482), GTF2H2B (NM_001042490 /// NM_001098728 /// NM 001098729 /// NM_001515), IGHG1 (NG 001019.5 ///NC 000014.8), IL18RAP (NM_003853), N4BP2 (NM_018177), PHACTR1 (NM_030948), RTKN2 (NM_145307), SLC16A1 (NM_003051), SOCS1 (NM_003745), SPAG17 (NM_206996), ST6GALNAC1 (NM_018414), STK17B (NM_004226), STT3B (NM_178862), STX16 (NM_001001433 /// NM_001134772 /// NM_001134773 /// NM_003763), TBC1D12 (NM_015188), TRIM4 (NM_033017 /// NM_033091), UACA (NM_001008224 /// NM_018003), and WHAMML2 (NR_026589) is correlative with or indicates that the patient has experienced or is at risk for experiencing lacunar stroke.

In various embodiments, the expression levels of a plurality of exon/splice variant biomarkers are co-determined together with the expression levels of a plurality of genes useful in the determination of whether a patient has experienced or has a predisposition to experience a hemorrhagic transformation. In varying embodiments, detecting an increase of the expression level of one or more biomarkers (e.g., 1, 2, 3, 4, 5 or 6 biomarkers) selected from the group consisting of MARCH7, SMAD4, AREG and INPP5D, and/or a decrease of the expression level of one or more biomarkers selected from the group consisting of TNFSF15 and MCFD22, compared to the control level of expression indicates that the patient suffers from or is at risk of experiencing hemorrhagic transformation of ischemic stroke. In some embodiments the methods further comprise determining a level of expression of a plurality of biomarkers (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23 or all biomarkers) selected from the group consisting of MARCH7, SMAD4, AREG, INPP5D, IRAK3, PELI1, CPD, PRKDC, GAFA3, AMACR, MKLN1, IQCK, TSC22D2, TAF8, POLH, SYTL3, EXOC6, RIF1, RNF144B, ATXN1L, TSPYL1, RAPGEF2, MTPAP, ABHD12B, LRRC18, LOC151438, NCRNA00081, TNFSF15 and MCFD22, wherein an increase of the expression level of one or more biomarkers selected from the group consisting of MARCH7, SMAD4, AREG, INPP5D, IRAK3, PELI1, CPD, PRKDC, GAFA3, AMACR, MKLN1, TSC22D2, TAF8, SYTL3, EXOC6, RIF1, RNF144B, RAPGEF2, ABHD12B, LRRC18, LOC151438 and NCRNA00081, and/or a decrease of the expression level of one or more biomarkers selected from the group consisting of TNFSF15 MCFD22, IQCK, POLH, ATXN1L, TSPYL1 and MTPAP compared to a control level of expression indicates that the patient suffers from or is at risk of experiencing hemorrhagic transformation of ischemic stroke, thereby diagnosing the occurrence of hemorrhagic transformation of ischemic stroke or the predisposition for experiencing hemorrhagic transformation of ischemic stroke.

4. Comparison to a Control Level of Expression

The expression of the ischemic stroke/ICH-associated biomarkers are compared to a control level of expression. As appropriate, the control level of expression can be the expression level of the same ischemic stroke/ICH-associated biomarker in an otherwise healthy individual (e.g., in an individual who has not experienced and/or is not at risk of experiencing ischemic stroke/ICH). In some embodiments, the control level of expression is the expression level of a plurality of stably expressed endogenous reference biomarkers, as described herein or known in the art. In some embodiments, the control level of expression is a predetermined threshold level of expression of the same ischemic stroke/ICH-associated biomarker, e.g., based on the expression level of the biomarker in a population of otherwise healthy individuals. In some embodiments, the expression level of the ischemic stroke/ICH-associated biomarker and the ischemic stroke/ICH-associated biomarker in an otherwise healthy individual are normalized to (i.e., divided by), e.g., the expression levels of a plurality of stably expressed endogenous reference biomarkers.

In varying embodiments, a subject may experience a vascular event that may be incorrectly diagnosed as ischemic stroke/ICH. In assessing a patient with a possible ischemic stroke or intracerebral hemorrhage, sometimes patients will have events that seem like ischemic stroke/ICH but are not - for example, a simple faint. Such patients will have a biomarker profile that is negative for stroke. To determine and distinguish subjects who have not experienced an ischemic stroke/ICH from subjects who have experienced an ischemic stroke or an intracerebral hemorrhage, provided herein are exon or splice variant biomarkers that identify subjects who have not experienced ischemic stroke or an intracerebral hemorrhage as distinguished from subjects who likely have experienced an ischemic stroke and intracerebral hemorrhage. These exon or splice variant biomarkers facilitate determining and distinguishing those patients who did not have an ischemic stroke or an intracerebral hemorrhage, even if presenting with one or more symptoms that might be diagnosed as ischemic stroke/ICH.

Accordingly, in varying embodiments, an increased expression level in comparison to a control of one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or all), ischemic stroke/ICH-associated biomarkers of Table 1E indicates that the subject has not or is unlikely to have experienced, ischemic stroke/ICH. High levels of expression of the exon or splice variant biomarkers, e.g., as compared to historical controls, indicate that the subject has not or is unlikely to have experienced, ischemic stroke/ICH. Low levels of expression of these control exon or splice variant biomarkers, e.g., as compared to historical controls, indicate that the subject has or is likely to have experienced ischemic stroke/ICH.

TABLE 1E Exon Usage Upregulated in Subjects Who Have Not Experienced ischemic Stroke/ICH Marker ID Gene Symbol chr20.32880178-32880361>AHCY AHCY chr2.242611606-242612018>ATG4B ATG4B chr9.96866557-96866669>PTPDC1 PTPDC1 chr17.42982993-42984758>GFAP GFAP chr22.41252435-41253038>ST13 ST13 chr1.53416427-53416560>SCP2 SCP2 chr6.32806430-32806549>TAP2andHLA-DOB TAP2 and HLA-DOB chr14.19683027-19683436>DUXAP10 DUXAP10 chr9.95018962-95019084>IARS IARS chr19.39138368-39138549>ACTN4 ACTN4 chr9.140473077-140473342>WDR85 WDR85 chrX.48367956-48368346>PORCN PORCN chr2.101606718-101606910>NPAS2 NPAS2 chr7.101475858-101476867>snorkar snorkar chr19.45543176-45543571>SFRS16 SFRS16 chr18.28642978-28643441>DSC2 DSC2 chr22.36892014-36892257>FOXRED2andTXN2 FOXRED2 and TXN2 chr18.43417478-43417852>SIGLEC15 SIGLEC15

In some embodiments, the overexpression or underexpression of a ischemic stroke/ICH-associated biomarker is determined with reference to the expression of the same ischemic stroke/ICH-associated biomarker in an otherwise healthy individual. For example, a healthy or normal control individual has not experienced and/or is not at risk of experiencing ischemic stroke/ICH. The healthy or normal control individual generally has not experienced a vascular event (e.g., cardioembolic stroke, large vessel stroke, lacunar stroke, TIA, ischemic stroke, myocardial infarction, peripheral vascular disease, venous thromboembolism or intracerebral hemorrhage). The healthy or normal control individual generally does not have one or more vascular risk factors (e.g., hypertension, diabetes mellitus, hyperlipidemia, or tobacco smoking). As appropriate, the expression levels of the target ischemic stroke/ICH-associated biomarker in the healthy or normal control individual can be normalized (i.e., divided by) the expression levels of a plurality of stably expressed endogenous reference biomarkers.

In some embodiments, the overexpression or underexpression of a ischemic stroke/ICH-associated biomarker is determined with reference to one or more stably expressed endogenous reference biomarkers. Internal control biomarkers or endogenous reference biomarkers are expressed at the same or nearly the same expression levels in the blood of patients who have experienced ischemic stroke/ICH as compared to control patients. Target biomarkers are expressed at higher or lower levels in the blood, serum and/or plasma of patients who have experienced or are at risk of experiencing ischemic stroke/ICH. The expression levels of the target biomarker to the reference biomarker are normalized by dividing the expression level of the target biomarker to the expression levels of a plurality of stably expressed endogenous reference biomarkers. The normalized expression level of a target biomarker can be used to predict the occurrence or lack thereof of ischemic stroke/ICH, and/or the cause of the ischemic stroke/ICH.

In some embodiments, the expression level of the ischemic stroke/ICH-associated biomarker (e.g., from Tables 1A-1D and biomarkers associated with cardioembolic stroke, atherothrombotic stroke, lacunar stroke, transient ischemic attack (TIA), hemorrhagic transformation described herein) from a patient suspected of having or experiencing an ischemic and from a control patient are normalized with respect to the expression levels of a plurality of stably expressed endogenous reference biomarkers. The expression levels of the normalized expression of the ischemic stroke/ICH-associated biomarkers are compared to the expression levels of the normalized expression of the same ischemic stroke/ICH-associated biomarker in a control patient. The determined fold change in expression =normalized expression of target biomarker in the ischemic stroke/ICH patient/ normalized expression of target biomarker in control patient. In varying embodiments, ischemic stroke/ICH-associated biomarker of interest (e.g., whole gene or exon/slice variant/isoform) is divided by the geometric average of the stably expressed endogenous reference biomarkers. If the normalized values are similar to historical controls (e.g., within two standard deviations), then the samples from such patients are diagnosed as indicating that the individual has not experienced and/or is not at risk of experiencing an ischemic stroke or intracerebral hemorrhage. If the expression levels of these exons are higher or lower than expected from historical controls (e.g., greater than two standard deviations), then the samples from such patients are diagnosed as indicating that the individual has experienced and/or is at risk of experiencing an ischemic stroke or intracerebral hemorrhage. In varying embodiments, software may be employed involving Support Vector Machine (SVM) or PAM signature determination and determining which side of the hyperplane subjects falls into for classification as having an ischemic stroke or an ICH. Overexpression or underexpression of the normalized ischemic stroke/ICH-associated biomarker in the ischemic stroke/ICH patient by at least about 1.2-fold, e.g., at least about 1.3-fold, 1.4-fold, 1.5-fold, 1.6-fold, 1.7-fold, 1.8-fold, 1.9-fold, 2.0-fold, or more, in comparison to the expression levels of the normalized ischemic stroke/ICH-associated biomarker in a healthy control patient indicates that the patient has experienced or is at risk of experiencing an ischemic stroke/ICH.

The biomarkers of Table 1E can also be normalized in comparison to internal control biomarkers or stably expressed endogenous reference biomarkers, as described above. The control exon biomarkers in Table 1E (upregulated in subjects who have not experienced ischemic stroke/ICH) can be divided by the geometric average of the endogenous control exons. If the normalized expression levels of the biomarkers listed in Table 1E are similar to historical controls (e.g., within two standard deviations), then the samples from these patients are diagnosed as controls who have not experienced or are unlikely to experience ischemic stroke or intracerebral hemorrhage. That is, the biomarkers of Table 1E are expressed at higher levels in controls compared to patients with ischemic stroke or intracerebral hemorrhage. If the expression levels of these exons are lower than expected from historical controls (greater than two standard deviations), then the samples from these patients are diagnosed as controls who have experienced or are likely to experience ischemic stroke or intracerebral hemorrhage. Additional biomarkers (e.g., from Tables 1A-1D and biomarkers associated with cardioembolic stroke, atherothrombotic stroke, lacunar stroke, transient ischemic attack (TIA), hemorrhagic transformation described herein) can then be used to distinguish whether the patient had an ischemic stroke or an intracerebral hemorrhage. The biomarkers of Table 1E are expressed at higher levels in subjects who have not experienced ischemic stroke/ICH compared to ischemic stroke and hemorrhage patients. They are thus lower in ischemic stroke and hemorrhage patients compared to controls. The expression of the biomarkers of Table 1E can be normalized to or divided by the expression of stably expressed endogenous reference biomarkers, described herein. If low levels of expression of the biomarkers of Table 1E compared to a normalized control are detected, this indicates the subject has experienced or is at risk to experience ischemic stroke or intracerebral hemorrhage. If higher levels of expression of the biomarkers of Table 1E compared to a normalized control are detected this indicates the subject has not experienced or is not at risk to experience ischemic stroke or intracerebral hemorrhage.

In some embodiments, the control level of expression is a predetermined threshold level. The threshold level can correspond to the level of expression of the same ischemic stroke/ICH-associated biomarker in an otherwise healthy individual or a population of otherwise healthy individuals, optionally normalized to the expression levels of a plurality of stably expressed endogenous reference biomarkers. After expression levels and normalized expression levels of the ischemic stroke/ICH-associated biomarkers are determined in a representative number of otherwise healthy individuals and individuals predisposed to experiencing ischemic stroke/ICH, normal and ischemic stroke/ICH-predisposed expression levels of the ischemic stroke/ICH-associated biomarkers can be maintained in a database, allowing for determination of threshold expression levels indicative of the presence or absence of risk to experience ischemic stroke/ICH or the occurrence of ischemic stroke/ICH. If the predetermined threshold level of expression is with respect to a population of normal control patients, then overexpression or underexpression of the ischemic stroke/ICH-associated biomarker (usually normalized) in the patient by at least about 1.2-fold, e.g., at least about 1.3-fold, 1.4-fold, 1.5-fold, 1.6-fold, 1.7-fold, 1.8-fold, 1.9-fold, 2.0-fold, or more, in comparison to the threshold level indicates that the patient has experienced or is at risk of experiencing ischemic stroke/ICH. If the predetermined threshold level of expression is with respect to a population of patients known to have experienced an ischemic stroke/ICH or known to be at risk for experiencing ischemic stroke/ICH, then an expression level in the patient suspected of experiencing ischemic stroke/ICH that is approximately equal to the threshold level (or overexpressed or underexpressed greater than the threshold level of expression), indicates that the patient has experienced or is at risk of experiencing an ischemic stroke/ICH.

With respect to the stably expressed endogenous reference biomarkers used for comparison, preferably, the endogenous reference biomarkers are stably expressed in blood. Exemplary endogenous reference biomarkers that find use are published, e.g., in Stamova, et al., BMC Medical Genomics (2009) 2:49. Additional endogenous reference biomarkers include without limitation, e.g., GAPDH, ACTB, B2M, HMBS, PPIB, USP7, MAPRE2, CSNK1G2, SAFB2, PRKAR2A, PI4KB, CRTC1, HADHA, MAP1LC3B, KATS, CDC2L1 /// CDC2L2, GTSE1, CDC2L1 /// CDC2L2, TCF25, CHP, LRRC40, hCG_2003956 /// LYPLA2 /// LYPLA2P1, DAXX, UBE2NL, EIF 1, KCMF1, PRKRIP1, CHMP4A, TMEM184C, TINF2, PODNL1, FBXO42, LOC441258, RRP1, Cl0orf104, ZDHHCS, C9orf23, LRRC45, NACC1, LOC100133445 /// LOC115110, PEX16. In some embodiments, the expression levels of a plurality of stably expressed endogenous reference biomarkers are determined as a control. In some embodiments, the expression levels of at least about 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, or more, stably expressed endogenous reference biomarkers described herein or known in the art, are determined as a control.

In some embodiments, the expression levels of the stably expressed endogenous reference biomarkers GAPDH, ACTB, B2M, HMBS and PPIB are determined as a control. In some embodiments, the expression levels of 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, or more, endogenous reference biomarkers selected from the group consisting of USP7, MAPRE2, CSNK1G2, SAFB2, PRKAR2A, PI4KB, CRTC1, HADHA, MAP1LC3B, KAT5, CDC2L1 /// CDC2L2, GTSE1, CDC2L1 /// CDC2L2, TCF25, CHP, LRRC40, hCG_2003956 /// LYPLA2 /// LYPLA2P1, DAXX, UBE2NL, EIF1, KCMF1, PRKRIP1, CHMP4A, TMEM184C, TINF2, PODNL1, FBXO42, LOC441258, RRP1, Cl0orf104, ZDHHCS, C9orf23, LRRC45, NACC1, LOC100133445 /// LOC115110, PEX16 are determined as a control.

5. Methods of Detecting Biomarkers Associated with Ischemic stroke/ICH

Gene expression may be measured using any method known in the art. One of skill in the art will appreciate that the means of measuring gene expression is not a critical aspect of the invention. The expression levels of the biomarkers can be detected at the transcriptional or translational (i.e., protein) level.

In some embodiments, the expression levels of the biomarkers are detected at the transcriptional level. A variety of methods of specific DNA and RNA measurement using nucleic acid hybridization techniques are known to those of skill in the art (see, Green and Sambrook, supra and Ausubel, supra) and may be used to detect the expression of the biomarkers set forth in Tables 1A-1E. Some methods involve an electrophoretic separation (e.g., Southern blot for detecting DNA, and Northern blot for detecting RNA), but measurement of DNA and RNA can also be carried out in the absence of electrophoretic separation (e.g., by dot blot). Southern blot of genomic DNA (e.g., from a human) can be used for screening for restriction fragment length polymorphism (RFLP) to detect the presence of a genetic disorder affecting a polypeptide of the invention. All forms of RNA can be detected, including, e.g., message RNA (mRNA), microRNA (miRNA), ribosomal RNA (rRNA) and transfer RNA (tRNA).

The selection of a nucleic acid hybridization format is not critical. A variety of nucleic acid hybridization formats are known to those skilled in the art. For example, common formats include sandwich assays and competition or displacement assays. Hybridization techniques are generally described in Hames and Higgins Nucleic Acid Hybridization, A Practical Approach, IRL Press (1985); Gall and Pardue, Proc. Natl. Acad. Sci. U.S.A., 63:378-383 (1969); and John et al. Nature, 223:582-587 (1969).

Detection of a hybridization complex may require the binding of a signal-generating complex to a duplex of target and probe polynucleotides or nucleic acids. Typically, such binding occurs through ligand and anti-ligand interactions as between a ligand-conjugated probe and an anti-ligand conjugated with a signal. The binding of the signal generation complex is also readily amenable to accelerations by exposure to ultrasonic energy.

The label may also allow indirect detection of the hybridization complex. For example, where the label is a hapten or antigen, the sample can be detected by using antibodies. In these systems, a signal is generated by attaching fluorescent or enzyme molecules to the antibodies or in some cases, by attachment to a radioactive label (see, e.g., Tij ssen, “Practice and Theory of Enzyme Immunoassays,” Laboratory Techniques in Biochemistry and Molecular Biology, Burdon and van Knippenberg Eds., Elsevier (1985), pp. 9-20).

The probes can be labeled either directly, e.g., with isotopes, chromophores, lumiphores, chromogens, or indirectly, such as with biotin, to which a streptavidin complex may later bind. Thus, the detectable labels used in the assays of the present invention can be primary labels (where the label comprises an element that is detected directly or that produces a directly detectable element) or secondary labels (where the detected label binds to a primary label, e.g., as is common in immunological labeling). Typically, labeled signal nucleic acids are used to detect hybridization. Complementary nucleic acids or signal nucleic acids may be labeled by any one of several methods typically used to detect the presence of hybridized polynucleotides. The most common method of detection is the use of autoradiography with ³H, ¹²⁵I, ³⁵S, ¹⁴C, or ³²P-labeled probes or the like.

Other labels include, e.g., ligands that bind to labeled antibodies, fluorophores, chemiluminescent agents, enzymes, and antibodies which can serve as specific binding pair members for a labeled ligand. An introduction to labels, labeling procedures and detection of labels is found in Polak and Van Noorden Introduction to Immunocytochemistry, 2nd ed., Springer Verlag, NY (1997); and in Haugland Handbook of Fluorescent Probes and Research Chemicals, a combined handbook and catalogue Published by Molecular Probes, Inc. (1996).

In general, a detector which monitors a particular probe or probe combination is used to detect the detection reagent label. Typical detectors include spectrophotometers, phototubes and photodiodes, microscopes, scintillation counters, cameras, film and the like, as well as combinations thereof. Examples of suitable detectors are widely available from a variety of commercial sources known to persons of skill in the art. Commonly, an optical image of a substrate comprising bound labeling moieties is digitized for subsequent computer analysis.

Most typically, the amount of RNA is measured by quantifying the amount of label fixed to the solid support by binding of the detection reagent. Typically, the presence of a modulator during incubation will increase or decrease the amount of label fixed to the solid support relative to a control incubation which does not comprise the modulator, or as compared to a baseline established for a particular reaction type. Means of detecting and quantifying labels are well known to those of skill in the art.

In preferred embodiments, the target nucleic acid or the probe is immobilized on a solid support. Solid supports suitable for use in the assays of the invention are known to those of skill in the art. As used herein, a solid support is a matrix of material in a substantially fixed arrangement.

For example, in one embodiment of the invention, microarrays are used to detect the pattern of gene expression. Microarrays provide one method for the simultaneous measurement of the expression levels of large numbers of genes. Each array has a reproducible pattern of a plurality of nucleic acids (e.g., a plurality of oligonucleotide probes that hybridize to a plurality of the biomarkers set forth in Tables 1A-1E) attached to a solid support. In one embodiment, the array contains a plurality of oligonucleotide probes that hybridize to a plurality of the biomarkers listed in Table 1A. In one embodiment, the array contains a plurality of oligonucleotide probes that hybridize to a plurality of the biomarkers listed in Table 1B. In one embodiment, the array contains a plurality of oligonucleotide probes that hybridize to a plurality of the biomarkers listed in Table 1C. In one embodiment, the array contains a plurality of oligonucleotide probes that hybridize to a plurality of the biomarkers listed in Table 1D. In one embodiment, the array contains a plurality of oligonucleotide probes that hybridize to a plurality of the biomarkers listed in Table 1E. In one embodiment, the array further contains a plurality of oligonucleotide probes that hybridize to a plurality of genes useful for diagnosing ischemic stroke, cardioembolic stroke, carotid stenosis, atrial fibrillation, transient ischemic attacks, lacunar stroke, and/or hemorrhagic transformation, as described herein and/or known in the art. In various embodiments, the array further contains a plurality of stably expressed endogenous reference biomarkers. Labeled RNA or DNA is hybridized to complementary probes on the array and then detected by laser scanning. Hybridization intensities for each probe on the array are determined and converted to a quantitative read-out of relative gene expression levels in ischemic stroke/ICH (e.g., correlative with or associative of ischemic stroke/ICH, or allowing the differentiation of a transient neurological event as ischemic or non-ischemic).

In some embodiments, a sample is obtained from a subject, total mRNA is isolated from the sample and is converted to labeled cRNA and then hybridized to an array. Relative transcript levels are calculated by reference to appropriate controls present on the array and in the sample. See Mahadevappa and Warrington, Nat. Biotechnol. 17, 1134-1136 (1999).

A variety of automated solid-phase assay techniques are also appropriate. For instance, very large scale immobilized polymer arrays (VLSIPS™), available from Affymetrix, Inc. (Santa Clara, Calif.) can be used to detect changes in expression levels of a plurality of genes involved in the same regulatory pathways simultaneously. See, Tijssen, supra., Fodor et al. (1991) Science, 251: 767- 777; Sheldon et al. (1993) Clinical Chemistry 39(4): 718-719, and Kozal et al. (1996) Nature Medicine 2(7): 753-759. Integrated microfluidic systems and other point-of-care diagnostic devices available in the art also find use. See, e.g., Liu and Mathies, Trends Biotechnol. (2009) 27(10):572-81 and Tothill, Semin Cell Dev Biol (2009) 20(1):55-62. Microfluidics systems for use in detecting levels of expression of a plurality of nucleic acids are commercially available, e.g., from NanoString Technologies (on the internet at nanostring.com), Applied Biosystems (Life Technologies) (appliedbiosystems.com) and Fluidigm (fluidigm.com).

Detection can be accomplished, for example, by using a labeled detection moiety that binds specifically to duplex nucleic acids (e.g., an antibody that is specific for RNA-DNA duplexes). One preferred example uses an antibody that recognizes DNA-RNA heteroduplexes in which the antibody is linked to an enzyme (typically by recombinant or covalent chemical bonding). The antibody is detected when the enzyme reacts with its substrate, producing a detectable product. Coutlee et al. (1989) Analytical Biochemistry 181:153-162; Bogulayski (1986) et al. J. Immunol. Methods 89:123-130; Prooijen-Knegt (1982) Exp. Cell Res. 141:397-407; Rudkin (1976) Nature 265:472-473, Stollar (1970) Proc. Nat'l Acad. Sci. USA 65:993-1000; Ballard (1982) Mol. Immunol. 19:793-799; Pisetsky and Caster (1982) Mol. Immunol. 19:645-650; Viscidi et al. (1988) J. Clin. Microbial. 41:199-209; and Kiney et al. (1989) J. Clin. Microbiol. 27:6-12 describe antibodies to RNA duplexes, including homo and heteroduplexes. Kits comprising antibodies specific for DNA:RNA hybrids are available, e.g., from Digene Diagnostics, Inc. (Beltsville, Md.).

In addition to available antibodies, one of skill in the art can easily make antibodies specific for nucleic acid duplexes using existing techniques, or modify those antibodies that are commercially or publicly available. In addition to the art referenced above, general methods for producing polyclonal and monoclonal antibodies are known to those of skill in the art (see, e.g., Paul (3rd ed.) Fundamental Immunology Raven Press, Ltd., NY (1993); Coligan, et al., Current Protocols in Immunology, Wiley Interscience (1991-2008); Harlow and Lane, Antibodies: A Laboratory Manual Cold Spring Harbor Press, NY (1988); Harlow and Lane, Using Antibodies, Cold Spring Harbor Press, NY (1999); Stites et al. (eds.) Basic and Clinical Immunology (4th ed.) Lange Medical Publications, Los Altos, CA, and references cited therein; Goding Monoclonal Antibodies: Principles and Practice (2d ed.) Academic Press, New York, N.Y., (1986); and Kohler and Milstein Nature 256: 495-497 (1975)). Other suitable techniques for antibody preparation include selection of libraries of recombinant antibodies in phage or similar vectors (see, Huse et al. Science 246:1275-1281 (1989); and Ward et al. Nature 341:544-546 (1989)). Specific monoclonal and polyclonal antibodies and antisera will usually bind with a dissociation constant (K_(D)) of at least about 0.1 μM, preferably at least about 0.01 μM or better, and most typically and preferably, 0.001 μM or better.

The nucleic acids used in this invention can be either positive or negative probes. Positive probes bind to their targets and the presence of duplex formation is evidence of the presence of the target. Negative probes fail to bind to the suspect target and the absence of duplex formation is evidence of the presence of the target. For example, the use of a wild type specific nucleic acid probe or PCR primers may serve as a negative probe in an assay sample where only the nucleotide sequence of interest is present.

The sensitivity of the hybridization assays may be enhanced through use of a nucleic acid amplification system that multiplies the target nucleic acid being detected. Examples of such systems include the polymerase chain reaction (PCR) system, in particular RT-PCR or real time PCR, and the ligase chain reaction (LCR) system. Other methods recently described in the art are the nucleic acid sequence based amplification (NASBA, Cangene, Mississauga, Ontario) and Q Beta Replicase systems. These systems can be used to directly identify mutants where the PCR or LCR primers are designed to be extended or ligated only when a selected sequence is present. Alternatively, the selected sequences can be generally amplified using, for example, nonspecific PCR primers and the amplified target region later probed for a specific sequence indicative of a mutation. High throughput multiplex nucleic acid sequencing or “deep sequencing” to detect captured expressed biomarker genes also finds use. High throughput sequencing techniques are known in the art (e.g., 454 Sequencing on the internet at 454.com). In varying embodiments, next generation sequencing, deep sequencing or ultra deep sequencing methodologies are applied. Deep sequencing data analysis is described, e.g., in “Deep Sequencing Data Analysis (Methods in Molecular Biology),” Noam Shomron (Editor), Humana Press; 2013 edition. Next generation sequencing is described, e.g., in “Next-Generation DNA Sequencing Informatics,” Stuart M. Brown (Editor), Cold Spring Harbor Laboratory Press; 1st edition (2013); “Next-generation Sequencing: Current Technologies and Applications,” Jianping Xu (Editor), Caister Academic Press (2014); Wilhelm, et al., Nature. (2008) 453:1239-1243; Nagalakshmi, et al., Science. (2008) 320:1344-1349; and Mortazavi, et al., Nat. Methods. (2008) 5:621-628.

In varying embodiments, the biomarkers (e.g., exons or splice variants or whole genes) are detected using RNA sequencing techniques. Methodologies for direct sequencing of RNA, e.g., without an intervening step of producing cDNA are known in the art, and described for example, in Nagalakshmi, et al., Curr Protoc Mol Biol. (Jan 2010) Chapter 4:Unit 4.11.1-13; Wang, et al ., Nat Rev Genet. (2009) 10(1):57-63; Kwok, et al, Trends Biochem Sci. (2015) 40(4):221-232; Ramsköld, et al., Methods Mol Biol. (2012) 802:259-74; Krupp, et al., Bioinformatics. (2012) 28(8):1184-5; Oudej ans, Clin Biochem. (2015) Mar 16. pii: S0009-9120(15)00081-8; Eij a Korpelainen and Jarno Tuimala, “RNA-seq Data Analysis: A Practical Approach (Chapman & Hall/CRC Mathematical and Computational Biology,” Chapman and Hall/CRC (Sep. 19, 2014); Ernesto Picardi, “RNA Bioinformatics (Methods in Molecular Biology),” Humana Press; 2015 edition (Jan. 11, 2015); and Shashikant Kulkarni and John Pfeifer, “Clinical Genomics,” Academic Press; 1 edition (Nov. 21, 2014).

An alternative means for determining the level of expression of the nucleic acids of the present invention is in situ hybridization. In situ hybridization assays are well known and are generally described in Angerer et al., Methods Enzymol. 152:649-660 (1987). In an in situ hybridization assay, cells, preferentially human cells, are fixed to a solid support, typically a glass slide. If DNA is to be probed, the cells are denatured with heat or alkali. The cells are then contacted with a hybridization solution at a moderate temperature to permit annealing of specific probes that are labeled. The probes are preferably labeled with radioisotopes or fluorescent reporters.

In other embodiments, quantitative RT-PCR is used to detect the expression of a plurality of the biomarkers set forth in one or more of Tables 1A-1E. In one embodiment, quantitative RT-PCR is used to further detect a plurality of the biomarkers useful for the diagnosis of ischemic stroke, cardioembolic stroke, carotid stenosis, atrial fibrillation, transient ischemic attacks, intracerebral hemorrhage and/or hemorrhagic transformation, as described herein and known in the art. A general overview of the applicable technology can be found, for example, in A-Z of Quantitative PCR, Bustin, ed., 2004, International University Line; Quantitative PCR Protocols, Kochanowski and Reischl, eds., 1999, Humana Press; Clinical Applications of PCR, Lo, ed., 2006, Humana Press; PCR Protocols: A Guide to Methods and Applications (Innis et al. eds. (1990)) and PCR

Technology: Principles and Applications for DNA Amplification (Erlich, ed. (1992)). In addition, amplification technology is described in U.S. Pat. Nos. 4,683,195 and 4,683,202. Methods for multiplex PCR, known in the art, are applicable to the present invention.

In varying embodiments, detection is accomplished by performing reverse transcription (RT) followed by a ligase detection reaction (LDR) with single-pair fluorescence resonance energy transfer (spFRET) (RT-LDR/spFRET). Methods for performing RT-LDR/spFRET are known in the art and described, e.g., in Peng, et al., Anal Chem. 2013 Aug. 20; 85(16):7851-8.

Accordingly, in one embodiment, provided is a reaction mixture comprising a plurality of polynucleotides which specifically hybridize (e.g., primers) to a plurality of nucleic acid sequences of the genes set forth in one or more of Tables 1A-1E. In some embodiments, the invention provides a reaction mixture further comprising a plurality of polynucleotides which specifically hybridize (e.g., primers) to a plurality of nucleic acid sequences of the genes useful for the diagnosis of ischemic stroke, cardioembolic stroke, carotid stenosis, atrial fibrillation, transient ischemic attacks, intracerebral hemorrhage and/or hemorrhagic transformation, as described herein and known in the art. In some embodiments, the reaction mixture is a PCR mixture, for example, a multiplex PCR mixture.

This invention relies on routine techniques in the field of recombinant genetics. Generally, the nomenclature and the laboratory procedures in recombinant DNA technology described below are those well-known and commonly employed in the art. Standard techniques are used for cloning, DNA and RNA isolation, amplification and purification. Generally enzymatic reactions involving DNA ligase, DNA polymerase, restriction endonucleases and the like are performed according to the manufacturer's specifications. Basic texts disclosing the general methods of use in this invention include Green and Sambrook et al., Molecular Cloning, A Laboratory Manual (4^(th) ed. 2012); Kriegler, Gene Transfer and Expression: A Laboratory Manual (1990); and Current Protocols in Molecular Biology (Ausubel et al., eds., 1987-2015, Wiley Interscience)).

For nucleic acids, sizes are given in either kilobases (kb) or base pairs (bp). These are estimates derived from agarose or acrylamide gel electrophoresis, from sequenced nucleic acids, or from published DNA sequences. For proteins, sizes are given in kilodaltons (kDa) or amino acid residue numbers. Proteins sizes are estimated from gel electrophoresis, from sequenced proteins, from derived amino acid sequences, or from published protein sequences.

Oligonucleotides that are not commercially available can be chemically synthesized according to the solid phase phosphoramidite triester method first described by Beaucage & Caruthers, Tetrahedron Letts. 22:1859-1862 (1981), using an automated synthesizer, as described in Van Devanter et. al., Nucleic Acids Res. 12:6159-6168 (1984). Purification of oligonucleotides is by either native acrylamide gel electrophoresis or by anion-exchange HPLC as described in Pearson & Reanier, J. Chrom. 255:137-149 (1983).

In some embodiments, the expression level of the biomarkers described herein are detected at the translational or protein level. Detection of proteins is well known in the art, and methods for protein detection known in the art find use. Exemplary assays for determining the expression levels of a plurality of proteins include, e.g., ELISA, flow cytometry, mass spectrometry (e.g., MALDI or SELDI), surface plasmon resonance (e.g., BiaCore), microfluidics and other biosensor technologies. See, e.g., Tothill, Semin Cell Dev Biol (2009) 20(1):55-62.

6. Providing Appropriate Treatment and Prevention Regimes to the Patient

Upon a positive determination or confirmation that a patient has experienced ischemic stroke/ICH, and a determination of the cause of the ischemic stroke/ICH, e.g., using established clinical procedures and/or the biomarkers provided herein and known in the art (e.g., employing biomarkers described in co-pending and co-owned U.S. Patent Publications Nos. 2015/0018234 (“BIOMARKERS FOR DIAGNOSING ISCHEMIA”); 2012/0316076 (“BIOMARKERS FOR THE DIAGNOSIS OF LACUNAR STROKE”); 2012/0065087 (“BIOMARKERS FOR DIAGNOSIS OF STROKE AND ITS CAUSES”); 2012/0015904 (“BIOMARKERS FOR DIAGNOSIS OF TRANSIENT ISCHEMIC ATTACKS”); and 2010/0197518 (“METHODS FOR DIAGNOSING ISCHEMIA”) for the diagnosis of ischemic stroke/ICH), the methods further provide for the step of prescribing, providing or administering a regime for the prophylaxis or treatment of ischemic stroke/ICH. By diagnosing the occurrence and/or the cause of ischemic stroke/ICH using the biomarkers described herein, a patient can rapidly receive treatment that is tailored to and appropriate for the type of ischemic stroke/ICH that has been experienced, or that the patient is at risk of experiencing.

For example, if the expression levels of the plurality of ischemic stroke/ICH-associated biomarkers indicate the occurrence or risk of ischemic stroke/ICH, a positive diagnosis of ischemic stroke/ICH can be supported or confirmed using methods known in the art. For example, the patient can be subject to MRI imaging of brain and vessels, additional blood tests, EKG, and/or echocardiogram. Patients who have experienced ischemic transient neurological events may undergo extensive evaluation of the heart, vasculature, blood and brain, and may receive stroke prevention therapy such as antiplatelet/anticoagulation, anti-hypertensive medication and lipid lowering therapy.

If the expression levels of the plurality of biomarkers indicate the occurrence or risk of an ischemic transient neurological event (e.g., transient ischemic attacks (TIA) or transient cerebral ischemia), the patient can be prescribed a regime of medications and/or life-style adjustments (e.g., diet, exercise, stress) to minimize risk factors can be recommended, including reducing blood pressure and cholesterol levels, and controlling diabetes. Several medications can be used to decrease the likelihood of a stroke after a transient ischemic attack. The medication selected will depend on the location, cause, severity and type of TIA, if TIA has occurred. For example, the patient may be prescribed a regime of an anti-platelet drug. The most frequently used anti-platelet medication is aspirin. An alternative to aspirin is the anti-platelet drug clopidogrel (Plavix). Some studies indicate that aspirin is most effective in combination with another anti-platelet drug. In some embodiments, the patient is prescribed a combination of low-dose aspirin and the anti-platelet drug dipyridamole (Aggrenox), to reduce blood clotting. Ticlopidine (Ticlid) is another anti-platelet medication that finds use to prevent or reduce the risk of stroke in patients who have experienced TIA. In some embodiments, the patient may be prescribed a regime of an anticoagulant. Exemplary anticoagulants include aspirin, heparin, warfarin, and dabigatran. Patients having a moderately or severely narrowed neck (carotid) artery, may require or benefit from carotid endarterectomy to clear carotid arteries of fatty deposits (atherosclerotic plaques) before another TIA or stroke can occur. In some embodiments, the patient may require or benefit from carotid angioplasty, or stenting.

In cases where a non-ischemic transient neurological event (TNE) is indicated, further evaluation to the cause of the non-ischemic TNE can be performed. For example, the subject can be given tests to determine if a migraine or seizure was experienced, and receive proper treatment. Patients with non-ischemic transient neurological events undergo different diagnostic evaluation and therapy, such as EEG and anti-seizure medication for seizures, and anti-migraine medication for migraines.

If the expression levels of the plurality of biomarkers indicate the occurrence or risk of cardioembolic stroke, the patient can be prescribed or administered a regime of an anticoagulant. Exemplary anticoagulants include aspirin, heparin, warfarin, and dabigatran.

If the expression levels of the plurality of biomarkers indicate the occurrence or risk of carotid stenosis, the patient can be prescribed or administered a regime of an anti-platelet drug. The most frequently used anti-platelet medication is aspirin. An alternative to aspirin is the anti-platelet drug clopidogrel (Plavix). Some studies indicate that aspirin is most effective in combination with another anti-platelet drug. In some embodiments, the patient is prescribed a combination of low-dose aspirin and the anti-platelet drug dipyridamole (Aggrenox), to reduce blood clotting. Ticlopidine (Ticlid) is another anti-platelet medication that finds use. Patients having a moderately or severely narrowed neck (carotid) artery, may require or benefit from carotid endarterectomy. This preventive surgery clears carotid arteries of fatty deposits (atherosclerotic plaques) to prevent a first or subsequent strokes. In some embodiments, the patient may require or benefit from carotid angioplasty, or stenting. Carotid angioplasty involves using a balloon-like device to open a clogged artery and placing a small wire tube (stent) into the artery to keep it open.

If the expression levels of the plurality of biomarkers indicate the occurrence or risk of atrial fibrillation, the patient can be prescribed a regime of an anti-coagulant (to prevent stroke) and/or a pharmacological agent to achieve rate control. Exemplary anticoagulants include aspirin, heparin, warfarin, and dabigatran. Exemplary rate control drugs include beta blockers (e.g., metoprolol, atenolol, bisoprolol), non-dihydropyridine calcium channel blockers (e.g., diltiazem or verapamil), and cardiac glycosides (e.g., digoxin).

If the expression levels of the plurality of ischemic stroke/ICH-associated biomarkers indicate the occurrence or risk of lacunar stroke, a positive diagnosis of lacunar stroke can be supported or confirmed using methods known in the art. For example, the patient can be subject to clinical evaluation (e.g., determination of one or more of the lacunar syndromes, including (1) Pure motor stroke/hemiparesis, (2) Ataxic hemiparesis, (3) Dysarthria/clumsy hand, (4) Pure sensory stroke, and (5) Mixed sensorimotor stroke), radiologic imaging, retinal imaging, evaluation of blood-brain barrier permeability, evidence of microhemorrhage and blood endothelial markers (e.g., (homocysteine, intercellular adhesion molecule 1 (ICAM1), thrombomodulin (TM), tissue factor (TF) and tissue factor pathway inhibitor (TFPI); Hassan, et al., Brain (2003) 126(Pt 2):424-32; and Hassan, et al., Brain. (2004) 127(Pt 1):212-9). Upon a positive diagnosis of lacunar stroke, the patient may be administered tissue plasminogen activator within three hours of experiencing ischemic stroke/ICH if the patient is without contraindications (i.e. a bleeding diathesis such as recent major surgery or cancer with brain metastases). High doses aspirin may be given within 48 hours of experiencing ischemic stroke/ICH. For long term prevention of recurrence, medical regimens may be aimed towards correcting the underlying risk factors for lacunar infarcts such as hypertension, diabetes mellitus and cigarette smoking.

If the expression levels of the plurality of ischemic stroke/ICH-associated biomarkers indicate the occurrence or risk of hemorrhagic transformation, a positive or negative diagnosis of hemorrhagic transformation of ischemic stroke can be supported or confirmed using methods known in the art. For example, the patient can be subject to MRI imaging of brain and vessels, additional blood tests, EKG, and/or echocardiogram. Patients who have experienced or who are at risk of hemorrhagic transformation of ischemic stroke may undergo extensive evaluation of the heart, vasculature, blood and brain, and may receive reduced dosages of tissue plasminogen activator (tPA), or administration of tPA may be withdrawn or discontinued. In some embodiments, patients who have experienced or who are at risk of hemorrhagic transformation of ischemic stroke may receive an interventional therapy instead of administration of tPA. In some embodiments, patients who have experienced or who are at risk of hemorrhagic transformation of ischemic stroke may receive may receive tPA co-administered with one or more pharmacological agents to prevent, inhibit, reduce and/or mitigate the symptoms of HT, e.g., minocycline, Edaravone, Fingolimide (see, Campos, et al., Stroke. (2013) 44(2):505-11), a matrix metalloproteinase (MMP) inhibitor (e.g., an inhibitor of MMP9), an anti-inflammatory agent and/or an antioxidant. Inhibitors of MMP9 that find use are known in the art and have been described, e.g., in Intl. Appl. Nos. PCT/US2010/023585, PCT/GB2003/002138, PCT/GB2003/000741, in U.S. Patent Publ. Nos. 2004/0147573, 2005/0113344, 2010/0098659, and in Tandon, et al, Bioinformation. (2011) 5(8):310-4, Tuccinardi, et al., Bioorg Med Chem. (2008) 16(16):7749-58. Patients who have not experienced or who are not at risk of hemorrhagic transformation of ischemic stroke may also undergo extensive evaluation of the heart, vasculature, blood and brain, and may receive tissue plasminogen activator (tPA).

7. Reaction Mixtures

Further provided are reaction mixtures for diagnosing ischemic stroke/ICH or a predisposition for developing ischemic stroke/ICH. In varying embodiments, the reaction mixtures comprise a plurality of nucleic acid probes or primer sets useful for the amplification of a plurality of biomarkers (e.g., 2, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100 biomarkers, or all listed biomarkers in the identified Table, e.g., e.g., Table 1A, Table 1B, Table 1C, Table 1D and/or Table 1E) of the biomarkers set forth in Tables 1A-E. In one embodiment, the reaction mixtures comprise a plurality of nucleic acid probes or primer sets that hybridize to a plurality of the biomarkers set forth in Table 1A. In one embodiment, the reaction mixtures comprise a plurality of nucleic acid probes or primer sets that hybridize to a plurality of the biomarkers set forth in Table 1B. In one embodiment, the reaction mixtures comprise a plurality of nucleic acid probes or primer sets that hybridize to a plurality of the biomarkers set forth in Table 1C. In one embodiment, the reaction mixtures comprise a plurality of nucleic acid probes or primer sets that hybridize to a plurality of the biomarkers set forth in Table 1D. In one embodiment, the reaction mixtures further comprise a plurality of nucleic acid probes or primer sets that hybridize to a plurality of the biomarkers set useful for the diagnosis of ischemic stroke, cardioembolic stroke, atherothrombotic stroke, carotid stenosis, lacunar stroke, atrial fibrillation, transient ischemic attacks (TIA), transient neurological events (TNEs), intracerebral hemorrhage and/or hemorrhagic transformation, as described herein. The probes may be immobilized on an array as described herein.

In varying embodiments, the reaction mixtures further can comprise appropriate buffers, salts, polymerases, dNTPs and other reagents to facilitate amplification and/or detection reactions (e.g., primers, labels) for amplifying one or more exons of a plurality of the biomarkers set forth in Tables 1A-E.

In some embodiments, the reaction mixtures can be provided in one or more reaction vessels that have aliquots of some or all of the reaction components of the reaction mixtures in them. Aliquots can be in liquid or dried (e.g., freeze-dried) form. Reaction vessels can include sample processing cartridges or other vessels that allow for the containment, processing and/or amplification of samples in the same vessel.

Further contemplated are kits comprising the reaction mixtures described above and herein.

8. Solid Supports and Kits

The invention further provides, a solid support comprising a plurality of nucleic acid probes that hybridize to a plurality (e.g., two or more, or all) of the biomarkers set forth in Tables 1A-E, and optionally stably expressed endogenous reference biomarkers, as described herein. For example, the solid support can be a microarray attached to a plurality of nucleic acid probes that hybridize to a plurality (e.g., two or more, or all) of the biomarkers set forth in Tables 1A-E, and optionally stably expressed endogenous reference biomarkers.

In various embodiments, the solid supports are configured to exclude genes not associated with or useful to the diagnosis, prediction or confirmation of ischemic stroke or ICH. For example, oligonucleotide probes that hybridize to genes or gene exons/splice variants/isoforms that are overexpressed or underexpressed less than 1.2-fold in subjects with ischemic stroke/ICH in comparison to a control level of expression can be excluded from the present solid supports. In some embodiments, oligonucleotide probes that hybridize to genes or gene exons that are overexpressed or underexpressed less than 1.2-fold in subjects with ischemic stroke, including transient cerebral ischemia, lacunar stroke, cardioembolic stroke, atherothrombotic stroke, TIA, TNE, carotid stenosis, and stroke subsequent to atrial fibrillation, in comparison to a control level of expression can be excluded from the present solid supports.

In various embodiments, the solid supports are configured to include only oligonucleotide probes that hybridize to genes or gene exons associated with or useful to the diagnosis, prediction or confirmation of ischemic stroke and/or ICH. For example, in some embodiments, only oligonucleotide probes that hybridize to genes or gene exons that are overexpressed or underexpressed more than 1.2-fold in subjects with ischemic stroke/ICH in comparison to a control level of expression are included in the present solid supports. In some embodiments, only oligonucleotide probes that hybridize to genes or gene exons that are overexpressed or underexpressed more than 1.2-fold in subjects with ICH or ischemic stroke (e.g., including transient cerebral ischemia, lacunar stroke, cardioembolic stroke, atherothrombotic stroke, TIA, TNE, carotid stenosis and stroke subsequent to atrial fibrillation), in comparison to a control level of expression are included in the present solid supports.

The solid support may optionally further comprise a plurality of oligonucleotide probes that hybridize to a plurality (e.g., two or more, or all) of the biomarkers useful for the diagnosis of ICH/ischemic stroke (e.g., cardioembolic stroke, carotid stenosis, and/or atrial fibrillation), as described herein. In various embodiments, the solid support comprises 5000, 4000, 3000, 2000, 1000 or fewer (e.g., 900, 800, 700, 600, 500 or fewer) nucleic acid probes that hybridize to a plurality of ischemic stroke/ICH-associated genes, as described herein. The solid support may be a component in a kit.

The invention also provides kits for diagnosing ischemic stroke/ICH or a predisposition for developing ischemic stroke/ICH. For example, the invention provides kits that include one or more reaction vessels that have aliquots of some or all of the reaction components of the reaction mixtures in them. Aliquots can be in liquid or dried form. Reaction vessels can include sample processing cartridges or other vessels that allow for the containment, processing and/or amplification of samples in the same vessel. The kits may comprise a plurality of nucleic acid probes or primer sets that hybridize to a plurality (e.g., two or more, or all) of the biomarkers set forth in Tables 1A-E. In one embodiment, the kits comprise a plurality of nucleic acid probes or primer sets that hybridize to a plurality of the biomarkers set forth in Table 1A. In one embodiment, the kits comprise a plurality of nucleic acid probes or primer sets that hybridize to a plurality of the biomarkers set forth in Table 1B. In one embodiment, the kits comprise a plurality of nucleic acid probes or primer sets that hybridize to a plurality of the biomarkers set forth in Table 1C. In one embodiment, the kits comprise a plurality of nucleic acid probes or primer sets that hybridize to a plurality of the biomarkers set forth in Table 1D. In one embodiment, the kits further comprise a plurality of nucleic acid probes or primer sets that hybridize to a plurality of the biomarkers set useful for the diagnosis of ischemic stroke, cardioembolic stroke, atherothrombotic stroke, carotid stenosis, lacunar stroke, atrial fibrillation, transient ischemic attacks (TIA), transient neurological events (TNEs), intracerebral hemorrhage and/or hemorrhagic transformation, as described herein. The probes may be immobilized on an array as described herein.

In addition, the kit can comprise appropriate buffers, salts and other reagents to facilitate amplification and/or detection reactions (e.g., primers, labels) for determining the expression levels of a plurality of the biomarkers set forth in Tables 1A-E. In one embodiment, the kit comprises appropriate buffers, salts and other reagents to facilitate amplification and/or detection reactions (e.g., primers, labels) for determining the expression levels of a plurality of the biomarkers set forth in Table 1A. In one embodiment, the kit comprises appropriate buffers, salts and other reagents to facilitate amplification and/or detection reactions (e.g., primers) for determining the expression levels of a plurality of the biomarkers set forth in Table 1B. In one embodiment, the kit comprises appropriate buffers, salts and other reagents to facilitate amplification and/or detection reactions (e.g., primers, labels) for determining the expression levels of a plurality of the biomarkers set forth in Table 1C. In one embodiment, the kit comprises appropriate buffers, salts and other reagents to facilitate amplification and/or detection reactions (e.g., primers) for determining the expression levels of a plurality of the biomarkers set forth in Table 1D. In one embodiment, the kit further comprises appropriate buffers, salts and other reagents to facilitate amplification and/or detection reactions (e.g., primers) for determining the expression levels of a plurality of the biomarkers useful for the diagnosis of ischemic stroke, cardioembolic stroke, atherothrombotic stroke, lacunar stroke, carotid stenosis, atrial fibrillation, and/or transient ischemic attacks (TIA), transient neurological events (TNEs) as described herein. The kits can also include written instructions for the use of the kit.

In one embodiment, the kits comprise a plurality of antibodies that bind to a plurality of the biomarkers set forth in Tables 1A-E. The kits may further comprise a plurality of antibodies that bind to a plurality of the biomarkers useful for the diagnosis of ischemic stroke, cardioembolic stroke, carotid stenosis, atrial fibrillation, transient ischemic attacks (TIA), transient neurological events (TNEs), intracerebral hemorrhage and/or hemorrhagic transformation, as described herein. The antibodies may or may not be immobilized on a solid support, e.g., an ELISA plate.

EXAMPLES

The following examples are offered to illustrate, but not to limit the claimed invention.

Example 1 Intracerebral Hemorrhage and Ischemic Stroke of Different Etiologies Have Distinct Alternatively Spliced mRNA Profiles in Blood Abstract

Background: Whole transcriptome studies have used 3′-biased expression microarrays to study genes regulated in blood of ischemic stroke patients. However, alternatively spliced messenger RNA isoforms have not been investigated for ischemic stroke or intracerebral hemorrhage (ICH) in animals or humans. Alternative splicing is the mechanism whereby a single gene's exons combine to produce distinct mRNA and protein isoforms. RNA-sequencing (RNA-Seq) was used to determine if alternative splicing varies for ICH and different ischemic stroke causes (cardioembolic, large vessel, lacunar) as compared to each other and controls.

Methods: Paired-end RNA-Seq was performed using Illumina Solexa technology to a depth of 200x10⁶reads for splicing analysis on twenty whole-blood samples. Differential alternative splicing was assessed using 1-way-ANOVA (FDR p<0.05). Differential exon-usage was calculated between each group (p<0.0005; (fold change|>1.2).

Results: 412 genes displayed differential alternative splicing among the groups. They were involved in cellular immune response, cell death and cell survival pathways implicated in stroke. Distinct expression signatures based on usage of 308 exons (292 genes) differentiated the groups.

Conclusions: This pilot study demonstrates alternatively spliced genes from whole blood differ in ICH compared to ischemic stroke, and differ between different ischemic stroke etiologies.

Methods

Stroke patients and control subjects were randomly selected from all those recruited at the UC Davis Medical Center between 2008 and 2012. Stroke patients were chosen to represent the major ischemic stroke etiologies (cardioembolic, large vessel, lacunar) or had intracerebral hemorrhages (ICH). Control subjects were selected to match the stroke subjects by age, race and sex, to have vascular risk factors and no cardiovascular events. All subjects provided Informed Consent. The UCD Institutional Review Board approved this study. IS diagnosis and causes were assessed as previously described [5, 9]. ICH patients had deep ICH confirmed by CT and/or MRI brain scans, and were associated with hypertension without evidence of vascular malformation, tumor or aneurysm. Controls had vascular risk factors without evidence of stroke. Blood was drawn into PAXgene tubes at 5.8 to 101.2 h following IS or ICH. RNA from whole blood was isolated as previously described [3].

Whole blood RNA was used to prepare mRNA libraries using the TruSeq RNA Sample Prep v2 kit and protocol (Illumina). Paired-end 100bp RNA-Seq reads on whole blood RNA were obtained by Illumina Solexa sequencing by synthesis on Illumina HiSeq2000 to a depth of 200×10⁶ reads. Bowtie 2 was used to map reads to a reference genome (Hg19) and generate bam files for analysis [10]. RNA transcript quantification was performed using Hg19 AceView transcripts in Partek Genomics Suite 6.6 RNA-Seq workflow. DAS was determined with ANOVA on Group (FDR p<0.05), and differential exon-usage was assessed between each two groups (p<0.0005, |fold change|>|1.2|).

Principal Component Analysis (PCA) and Hierarchical Clustering were performed in Partek. Ingenuity Pathway Analysis (IPA®) and DAVID identified regulated pathways and processes as described previously [6].

Results

Subject Demographics. Subject demographics and clinical characteristics are presented in Table 2. Only Caucasian males were studied because of the small group sizes. Demographics for age, time since event for IS or ICH, and vascular risk factors were not significantly different. Coverage of a wide range of post-stroke biology was obtained by selecting patients with early (5.8 hours) through late (101.2 hours) blood draw times after stroke event. Although this time range seems wide, means are similar between stroke groups. Cardioembolic post-event blood draw times were, on average, 33.7 hours; large vessel averaged 47.4 hours; lacunar averaged 34.6 hours; and ICH averaged 29.4 hours (Table 2).

TABLE 2 Subjects' Characteristics. Ischemic Stroke Intracerebral Cardioembolic Large Vessel Lacunar Hemorrhage Controls Subjects, no. (total n = 20) 4 4 4 4 4 Age, years (mean ± SD) 62.3 ± 9.6  61.0 ± 8.2  58.9 ± 9.0  60.1 ± 2.3  60.8 ± 9.2 Time since event, hours (mean ± SD) 33.7 ± 18.9 47.4 ± 47.8 34.6 ± 23.7 29.4 ± 15.5 N/A Hypertension, no. 4 3 2 3 3 Diabetes, no. 2 2 0 0 1 Hyperlipidemia, no. 3 2 2 0 2

RNA Sequencing Alignments. RNA sequencing alignments statistics for all samples among the five groups are presented in Table 3. Cardioembolic stroke samples had on average, 1.60E+08 alignments; large vessel had 1.65E+08 alignments; lacunar stroke had 1.64E+08 alignments; and ICH and control each averaged 1.59E+08 alignments.

TABLE 3 RNA-Seq Reads All Samples Sequence Length 100 Average Quality per Read PH RED score 37 Total Sequence Reads Mean ± SD 1.95E+08 ± 1.30E+07 Total Alignments Mean ± SD 1.61E+08 ± 1.01E+07 % GC Alignments Mean ± SD 54.20 ± 1.91  Unmapped Sequences Mean ± SD 3.33E+07 ± 4.44E+06 % GC Unmapped Sequences Mean ± SD 61.60 ± 3.45  Ischemic Stroke Intracerebral Cardioembolic Large Vessel Lacunar Hemorrhage Controls Total Sequence Reads Mean ± SD 1.93E+08 ± 1.07E+07 1.99E+08 ± 1.14E+07 1.99E+08 ± 1.18E+07 1.91E+08 ± 1.53E+08 1.92E+08 ± 1.94E+09 Total Sequence Reads by Sample 1 177,117,828 203,837,628 203,564,103 191,131,791 185,714,780 2 195,150,937 182,750,587 213,336,146 199,832,252 218,687,770 3 198,658,650 209,078,152 188,188,692 169,147,880 172,555,000 4 200,504,201 198,375,293 190,420,476 202,961,105 192,521,761 Number of Alignments Mean ± SD 1.60E+08 ± 9.73E+06 1.65E+08 ± 1.25E+07 1.64E+08 ± 8.34E+06 1.59E+08 ± 1.18E+07 1.59E+08 ± 1.18E+07 CV (%) 6.073 7.61352 5.09486 7.42897 7.46071 Mean % GC ± SD 54.75 ± 2.36  55.75 ± 0.96  53.75 ± 1.89  52.00 ± 0.82  54.75 ± 1.26  Alignments by Sample 1 164,675,690 171,375,517 166,034,796 160,755,434 157,275,379 2 164,012,069 146,190,367 174,444,217 168,409,440 174,121,248 3 145,627,854 172,988,643 157,269,390 142,396,412 145,330,668 4 166,272,000 168,785,456 156,892,385 166,405,048 157,539,078 Number of Unmapped Sequences Mean ± SD 3.27E+07 ± 3.14E+06 3.37E+07 ± 3.28E+06 3.52E+07 ± 3.66E+06 3.13E+07 ± 4.05E+06 3.38E+07 ± 7.94E+06 Mean % GC ± SD 63.25 ± 2.63  62.25 ± 1.26  61.75 ± 1.89  57.25 ± 4.86  63.5 ± 2.38 Unmapped Sequences by Sample 1 35,828,511 32,462,111 37,529,307 30,376,357 28,439,401 2 34,646,581 36,560,220 38,891,929 31,422,812 44,566,522 3 31,489,974 36,089,509 30,919,302 26,751,468 27,224,332 4 28,878,937 29,589,837 33,528,091 36,556,057 34,982,683

Distinct Alternatively Spliced Transcriptomes from Whole Blood of Patients with ICH, Different IS Etiologies and Controls. 412 genes display DAS in the whole blood transcriptomes of patients with IS (cardioembolic, large vessel, and lacunar), ICH and controls (FDR p<0.05; Table 4). These genes are involved in cellular immunity, cytokine signaling and cell death and survival pathways (Table 5). Pathways with higher over-representation of DAS genes between groups include: CD28 signaling in T helper cells, CDC42 signaling, Nur77 signaling in T lymphocytes, fMLP signaling in neutrophils, and interferon signaling (Table 5). Molecular and cellular functions best representing the DAS genes are: cell death/survival of immune cells/leukocytes, cell-to-cell signaling and interaction, including activation, recruitment and adhesion of leukocytes, antigen presenting cells, activation of T lymphocytes, adhesion of vascular endothelial cells and immune response of neutrophils (Table 6).

Specific Exon-Usage Profiles for IS and ICH. Distinct differential expression signatures based on 308 exons (292 genes) (p<0.0005, fold change>|1.2|; Table 1) separated the three causes of IS, as well as ICH and controls (PCA FIG. 2A; Unsupervised Hierarchical Clustering FIG. 2B). Biological functions and networks represented by genes with highly expressed exons in each group (in FIG. 2B) are displayed in Table 8. Cardioembolic stroke genes with differential exon usage are involved in ion binding and transport, cellular assembly and organization. Large vessel genes are associated with cell death, transcription and chromatin remodeling. Lacunar stroke genes are associated with cellular compromise, cell cycle, cell death and survival. ICH genes are involved with protein transport and localization (Table 8).

TABLE 4 Genes (412) with Differential Alternative Splicing Among Large Vessel Ischemic Stroke (IS), Cardioembolic IS, Lacunar IS, Intracerebral Hemorrhage and Controls stepup alt- (alt- splicing splicing Gene Symbol Gene Name (Dx) (Dx)) MARCH7 membrane-associated ring finger (C3HC4) 7 1.18E−05 9.07E−04 SEPT15 septin 5 3.38E−05 2.16E−03 ABCA7 ATP-binding cassette, sub-family A (ABC1), member 7 3.37E−08 7.73E−06 ACSL4/KCNE1L acyl-CoA synthetase long-chain family member 4/KCNE1- 6.77E−05 3.66E−03 like ACTR2 ARP2 actin-related protein 2 homolog (yeast) 5.76E−20 2.57E−16 ACTR3 ARP3 actin-related protein 3 homolog (yeast) 1.29E−03 3.34E−02 ADCK2/NDUFB2 aarF domain containing kinase 2/NADH dehydrogenase 6.16E−05 3.42E−03 (ubiquinone) 1 beta subcomplex, 2, 8 kDa ADCY7 adenylate cyclase 7 6.29E−09 1.76E−06 ADD3 adducin 3 (gamma) 1.14E−05 8.90E−04 ADSS/TGIF2P1 adenylosuccinate synthase/TGFB-induced factor 4.63E−05 2.67E−03 homeobox 2 pseudogene 1 AKAP8 A kinase (PRKA) anchor protein 8 1.29E−03 3.34E−02 ANAPC13 anaphase promoting complex subunit 13 1.50E−03 3.70E−02 ANKRD12 ankyrin repeat domain 12 3.96E−06 3.97E−04 ANKRD13A ankyrin repeat domain 13A 7.49E−05 3.95E−03 ANXA1 annexin A1 8.66E−08 1.65E−05 ANXA7 annexin A7 8.70E−06 7.20E−04 AP1S2 adaptor-related protein complex 1, sigma 2 subunit 1.11E−03 2.93E−02 pseudogene; adaptor-related protein complex 1, sigma 2 subunit APAF1 apoptotic peptidase activating factor 1 1.80E−03 4.20E−02 APH1A anterior pharynx defective 1 homolog A (C. elegans) 1.32E−03 3.40E−02 APIP APAF1 interacting protein; similar to APAF1 interacting 1.35E−03 3.45E−02 protein APOBEC3A/ apolipoprotein B mRNA editing enzyme, catalytic 5.87E−04 1.81E−02 APOBEC3B polypeptide-like 3A/apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B ARCN1 archain 1 2.53E−04 9.85E−03 ARFIP1/FHDC1 ADP-ribosylation factor interacting protein 1/FH2 domain 1.69E−05 1.24E−03 containing 1 ARID4B/RBM34 AT rich interactive domain 4B (RBP1-like)/RNA binding 4.36E−05 2.56E−03 motif protein 34 ARL6IP5 ADP-ribosylation-like factor 6 interacting protein 5 2.89E−05 1.91E−03 ARNTL aryl hydrocarbon receptor nuclear translocator-like 1.83E−05 1.32E−03 ARPC3/ANAPC7 actin related protein 2/3 complex, subunit 3, 5.80E−11 3.45E−08 21 kDa/anaphase promoting complex subunit 7 ARPC4/TTLL3 actin related protein 2/3 complex, subunit 4, 20 kDa/tubulin 3.14E−11 2.16E−08 tyrosine ligase-like family member 3 ARPC5L actin related protein 2/3 complex, subunit 5-like 2.44E−04 9.56E−03 ATM similar to Serine-protein kinase ATM (Ataxia telangiectasia 6.24E−05 3.42E−03 mutated) (A-T, mutated); ataxia telangiectasia mutated ATP2B4 ATPase, Ca++ transporting, plasma membrane 4 2.42E−04 9.54E−03 ATP5B/SNORD59A/ ATP synthase, H+ transporting, mitochondrial F1 complex, 3.76E−10 1.46E−07 SNORD59B beta polypeptide/small nucleolar RNA, C/D box 59A/small nucleolar RNA, C/D box 59B ATP6V1G2/ ATPase, H+ transporting, lysosomal 13 kDa, V1 subunit 2.39E−06 2.51E−04 BAT1(DDX39B)/ G2/DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B/small SNORD84 nucleolar RNA, C/D box 84 ATXN1L/ ataxin 1-like/increased sodium tolerance 1 homolog (yeast) 8.77E−05 4.38E−03 KIAA0174(IST1) AZIN1 antizyme inhibitor 1 8.54E−04 2.38E−02 baboy 5.62E−04 1.76E−02 BAZ1A bromodomain adjacent to zinc finger domain, 1A 7.63E−04 2.21E−02 BAZ2B bromodomain adjacent to zinc finger domain, 2B 4.42E−04 1.49E−02 BTN2A2/BTN3A1 butyrophilin, subfamily 2, member A2/butyrophilin, 3.13E−06 3.21E−04 subfamily 3, member A1 C11orf73 chromosome 11 open reading frame 73 1.71E−03 4.08E−02 C15orf29 chromosome 15 open reading frame 29 5.37E−08 1.17E−05 C1orf59 chromosome 1 open reading frame 59 5.42E−05 3.03E−03 C1orf63 chromosome 1 open reading frame 63 1.10E−12 1.40E−09 C5orf15 chromosome 5 open reading frame 15 5.26E−04 1.67E−02 C6orf62 chromosome 6 open reading frame 62 1.51E−04 6.62E−03 C7orf27 chromosome 7 open reading frame 27 7.25E−04 2.11E−02 C9orf114 chromosome 9 open reading frame 114 2.31E−04 9.15E−03 C9orf72 chromosome 9 open reading frame 72 5.43E−04 1.71E−02 CAB39 calcium binding protein 39 9.34E−05 4.56E−03 CALM1 calmodulin 3 (phosphorylase kinase, delta); calmodulin 2 2.24E−07 3.77E−05 (phosphorylase kinase, delta); calmodulin 1 (phosphorylase kinase, delta) CALM2/C2orf61 calmodulin 2 (phosphorylase kinase, delta)/chromosome 2 3.70E−12 3.00E−09 open reading frame 61 CAPZA2 capping protein (actin filament) muscle Z-line, alpha 2 6.35E−04 1.91E−02 CARD8 caspase recruitment domain family, member 8 5.51E−08 1.17E−05 CBARA1 calcium binding atopy-related autoantigen 1 2.87E−04 1.08E−02 CCAR1 cell division cycle and apoptosis regulator 1 1.61E−05 1.19E−03 CCNDBP1 cyclin D-type binding-protein 1 3.17E−10 1.29E−07 CCNY cyclin Y 1.68E−04 7.13E−03 CCT8 similar to chaperonin containing TCP1, subunit 8 (theta); 2.19E−03 4.80E−02 chaperonin containing TCP1, subunit 8 (theta) CD164 CD164 molecule, sialomucin 1.82E−05 1.32E−03 CD244 CD244 molecule, natural killer cell receptor 2B4 6.82E−04 2.03E−02 CD300E CD300e molecule 1.05E−04 4.97E−03 CD36 CD36 molecule (thrombospondin receptor) 2.83E−07 4.60E−05 CD46 CD46 molecule, complement regulatory protein 4.46E−06 4.29E−04 CD47 CD47 molecule 4.97E−15 9.66E−12 CD53 CD53 molecule 1.52E−04 6.62E−03 CD58 CD58 molecule 2.07E−04 8.41E−03 CD74 CD74 molecule, major histocompatibility complex, class II 6.89E−04 2.03E−02 invariant chain CD86 CD86 molecule 1.60E−03 3.88E−02 CDC42SE1 CDC42 small effector 1 1.70E−06 1.97E−04 CDC42SE2 CDC42 small effector 2 3.58E−04 1.26E−02 CDKL3/PPP2CA cyclin-dependent kinase-like 3/protein phosphatase 2, 3.66E−05 2.26E−03 catalytic subunit, alpha isozyme CDKN1C cyclin-dependent kinase inhibitor 1C (p57, Kip2) 2.33E−05 1.59E−03 CECR1 cat eye syndrome chromosome region, candidate 1 6.88E−06 5.97E−04 CELF2 CUG triplet repeat, RNA binding protein 2 3.17E−04 1.14E−02 CFLAR/ CASP8 and FADD-like apoptosis regulator/RNA, U7 small 1.42E−08 3.64E−06 RNU7-45P nuclear 45 pseudogene CGGBP1 CGG triplet repeat binding protein 1 7.87E−05 4.06E−03 CHMP2B chromatin modifying protein 2B 1.42E−03 3.57E−02 CLDND1 claudin domain containing 1 2.13E−06 2.32E−04 CLEC7A C-type lectin domain family 7, member A 8.25E−10 3.02E−07 CLTC clathrin, heavy chain (Hc) 2.74E−04 1.04E−02 CNIH cornichon homolog (Drosophila) 1.84E−04 7.55E−03 CNOT6L CCR4-NOT transcription complex, subunit 6-like 6.04E−04 1.85E−02 CNOT7 CCR4-NOT transcription complex, subunit 7 2.15E−03 4.75E−02 CNOT8 CCR4-NOT transcription complex, subunit 8 3.00E−04 1.10E−02 COMMD2 canopy 2 homolog (zebrafish) 1.41E−03 3.55E−02 CRKL COMM domain containing 2 1.14E−03 3.00E−02 CSGALNACT2 chondroitin sulfate N-acetylgalactosaminyltransferase 2; 3.60E−05 2.26E−03 novel protein similar to chondroitin sulfate GalNAcT-2 (GALNACT-2) CTDSP2 similar to hCG2013701; CTD (carboxy-terminal domain, 5.61E−04 1.76E−02 RNA polymerase II, polypeptide A) small phosphatase 2 CTSS cathepsin S 1.46E−06 1.76E−04 CYBB cytochrome b-245, beta polypeptide 7.15E−09 1.94E−06 CYBRD1 cytochrome b reductase 1 2.31E−05 1.59E−03 CYLD cylindromatosis (turban tumor syndrome) 1.37E−03 3.47E−02 DAP3 death associated protein 3 2.13E−03 4.74E−02 DCP2 DCP2 decapping enzyme homolog (S. cerevisiae) 3.88E−07 5.69E−05 DDX19B/DDX19A DEAD (Asp-Glu-Ala-Asp) box polypeptide 19B/DEAD (Asp- 3.10E−04 1.13E−02 Glu-Ala-Asp) box polypeptide 19A DDX3X DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linked 1.37E−12 1.53E−09 DDX60L DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like 4.35E−06 4.27E−04 DEGS1 degenerative spermatocyte homolog 1, lipid desaturase 1.25E−04 5.67E−03 (Drosophila) DENND5A DENN/MADD domain containing 5A 3.64E−07 5.45E−05 DHX40 similar to DEAH (Asp-Glu-Ala-His) box polypeptide 40; 7.11E−04 2.08E−02 DEAH (Asp-Glu-Ala-His) box polypeptide 40 DMXL2 Dmx-like 2 7.29E−12 5.43E−09 DNAJB6 DnaJ (Hsp40) homolog, subfamily B, member 6 1.20E−04 5.52E−03 DNTTIP1 deoxynucleotidyltransferase, terminal, interacting protein 1 1.88E−03 4.29E−02 DPEP2/DPEP3 dipeptidase 2/dipeptidase 3 5.43E−05 3.03E−03 DPY30/MEM01 dpy-30 homolog (C. elegans)/mediator of cell motility 1 2.26E−03 4.91E−02 DPYD dihydropyrimidine dehydrogenase 8.13E−08 1.61E−05 DTX3L deltex 3-like (Drosophila) 3.95E−04 1.37E−02 DUSP22 similar to mitogen-activated protein kinase phosphatase x; 7.74E−04 2.21E−02 dual specificity phosphatase 22 DYNC1LI1 dynein, cytoplasmic 1, light intermediate chain 1 7.00E−04 2.06E−02 DYNC1LI2 dynein, cytoplasmic 1, light intermediate chain 2 3.68E−05 2.26E−03 DYX1C1/CCPG1 dyslexia susceptibility 1 candidate 1/cell cycle progression 7.61E−05 3.95E−03 1 EAPP E2F-associated phosphoprotein 5.17E−04 1.67E−02 ECHDC1 enoyl Coenzyme A hydratase domain containing 1 7.45E−06 6.34E−04 ECHDC2 enoyl Coenzyme A hydratase domain containing 2 9.29E−04 2.55E−02 EGLN1 egl nine homolog 1 (C. elegans) 2.12E−04 8.51E−03 EIF2AK2 eukaryotic translation initiation factor 2-alpha kinase 2 1.63E−03 3.91E−02 EIF2S1 eukaryotic translation initiation factor 2, subunit 1 alpha, 4.13E−04 1.42E−02 35 kDa ELP2 elongation protein 2 homolog (S. cerevisiae) 1.01E−05 8.06E−04 EMB embigin homolog (mouse) 1.03E−10 5.41E−08 EPHB4 EPH receptor B4 1.48E−03 3.67E−02 ERAP1 endoplasmic reticulum aminopeptidase 1 8.18E−05 4.13E−03 ERBB2IP erbb2 interacting protein 6.97E−05 3.73E−03 ERN1 endoplasmic reticulum to nucleus signaling 1 1.70E−03 4.07E−02 ETNK1 ethanolamine kinase 1 1.83E−03 4.23E−02 FAM111B/ family with sequence similarity 111, member B/family with 1.78E−03 4.16E−02 FAM111A sequence similarity 111, member A FAM118A family with sequence similarity 118, member A 9.23E−10 3.13E−07 FAM198B chromosome 4 open reading frame 18 2.90E−04 1.08E−02 FAM45A family with sequence similarity 45, member A 2.11E−04 8.51E−03 FBXL3 F-box and leucine-rich repeat protein 3 2.01E−04 8.22E−03 FBXL5 F-box and leucine-rich repeat protein 5 1.40E−06 1.71E−04 FCER1A Fc fragment of IgE, high affinity I, receptor for; alpha 6.21E−07 8.53E−05 polypeptide FKBP1A/SDCBP2 FK506 binding protein 1A, 12 kDa/syndecan binding protein 1.09E−03 2.89E−02 (syntenin) 2 FNTA farnesyltransferase, CAAX box, alpha 2.84E−08 6.86E−06 GALNT1 UDP-N-acetyl-alpha-D-galactosamine:polypeptideN- 3.80E−09 1.13E−06 acetylgalactosaminyltransferase 13 (GalNAc-T13); UDP-N- acetyl-alpha-D-galactosamine:polypeptide N- acetylgalactosaminyltransferase 1 (GalNAc-T1) GBP4/GBP7/ guanylate binding protein 4/guanylate binding protein 3.67E−05 2.26E−03 GBP2 7/guanylate binding protein 2, interferon-inducible GCA grancalcin, EF-hand calcium binding protein 2.92E−07 4.66E−05 GGNBP2 gametogenetin binding protein 2 1.12E−04 5.26E−03 GHITM growth hormone inducible transmembrane protein 9.44E−07 1.22E−04 GIT2 G protein-coupled receptor kinase interacting ArfGAP 2 5.73E−04 1.78E−02 GLRX glutaredoxin (thioltransferase) 5.22E−04 1.67E−02 GLUD1 glutamate dehydrogenase 1 4.22E−05 2.52E−03 GMCL1 germ cell-less homolog 1 (Drosophila)-like; germ cell-less 4.91E−04 1.62E−02 homolog 1 (Drosophila) GPX1 glutathione peroxidase 1 1.77E−03 4.15E−02 GSTK1 glutathione S-transferase kappa 1 1.77E−04 7.34E−03 GSTO1 glutathione S-transferase omega 1 4.25E−04 1.44E−02 GTF2I general transcription factor II, i; general transcription factor 1.39E−05 1.04E−03 II, i, pseudogene GZMA granzyme A (granzyme 1, cytotoxic T-lymphocyte- 1.27E−03 3.31E−02 associated serine esterase 3) H2AFZ H2A histone family, member Z 8.03E−04 2.26E−02 H3F3B H3 histone, family 3B (H3.3B); H3 histone, family 3A 1.90E−03 4.32E−02 pseudogene; H3 histone, family 3A; similar to H3 histone, family 3B; similar to histone H3.3B HBP1 HMG-box transcription factor 1 7.69E−04 2.21E−02 HDC histidine decarboxylase 1.26E−03 3.28E−02 HERC3 hect domain and RLD 3 4.70E−07 6.67E−05 HERC5 hect domain and RLD 5 1.03E−05 8.14E−04 hetira 7.84E−04 2.22E−02 HEXB hexosaminidase B (beta polypeptide) 3.00E−04 1.10E−02 HIPK3 homeodomain interacting protein kinase 3 2.01E−10 9.45E−08 HLA-DMA/ major histocompatibility complex, class II, DM alpha/major 5.32E−05 3.01E−03 HLA-DMB histocompatibility complex, class II, DM beta HLA-DQA1 similar to hCG2042724; similar to HLA class II 1.89E−03 4.31E−02 histocompatibility antigen, DQ(1) alpha chain precursor (DC-4 alpha chain); major histocompatibility complex, class II, DQ alpha 1 HLA-DRB1 major histocompatibility complex, class II, DR beta 4; major 2.35E−06 2.49E−04 histocompatibility complex, class II, DR beta 1 HMGB1 high-mobility group box 1; high-mobility group box 1-like 10 1.45E−03 3.64E−02 HMGCL/GALE 3-hydroxymethyl-3-methylglutaryl-CoA lyase/UDP- 1.02E−03 2.73E−02 galactose-4-epimerase HMGN4 high mobility group nucleosomal binding domain 4 7.64E−06 6.44E−04 HNRNPA2B1 heterogeneous nuclear ribonucleoprotein A2/B1 5.52E−06 4.93E−04 HNRNPAB heterogeneous nuclear ribonucleoprotein A/B 3.04E−04 1.11E−02 HNRNPH3 heterogeneous nuclear ribonucleoprotein H3 (2H9) 2.16E−06 2.32E−04 HP1BP3 heterochromatin protein 1, binding protein 3 1.62E−03 3.90E−02 HSD17B11/ hydroxysteroid (17-beta) dehydrogenase 11/hydroxysteroid 6.11E−04 1.86E−02 HSD17B13 (17-beta) dehydrogenase 13 HSD17B4/FAM170A hydroxysteroid (17-beta) dehydrogenase 4/family with 2.19E−05 1.52E−03 sequence similarity 170, member A HSPC157 long intergenic non-protein coding RNA 339/cell division cycle 42 1.01E−03 2.72E−02 (LINC00339)/CDC42 IDH1 isocitrate dehydrogenase 1 (NADP+), soluble 7.39E−06 6.34E−04 IFIH1 interferon induced with helicase C domain 1 5.00E−04 1.65E−02 IFNAR1 interferon (alpha, beta and omega) receptor 1 3.13E−04 1.13E−02 IFNGR1 interferon gamma receptor 1 3.75E−11 2.39E−08 IFRD1/C7orf53 interferon-related developmental regulator 1/leucine-rich 8.87E−04 2.44E−02 (LSMEM1) single-pass membrane protein 1 IGFBP7 insulin-like growth factor binding protein 7 3.17E−04 1.14E−02 IKZF1 IKAROS family zinc finger 1 (Ikaros) 1.72E−03 4.10E−02 ING4 inhibitor of growth family, member 4 1.09E−06 1.39E−04 IPMK inositol polyphosphate multikinase 5.25E−04 1.67E−02 IQGAP2 IQ motif containing GTPase activating protein 2 8.51E−04 2.38E−02 ITGA4 integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 5.23E−06 4.77E−04 receptor) JAK2 Janus kinase 2 5.67E−07 7.92E−05 JMJD1C jumonji domain containing 1C 1.42E−05 1.05E−03 KIAA1033 KIAA1033 7.58E−05 3.95E−03 kihire 2.02E−03 4.56E−02 KLF13 Kruppel-like factor 13 1.75E−03 4.14E−02 LACTB lactamase, beta 2.22E−07 3.77E−05 LAPTM4A lysosomal protein transmembrane 4 alpha 1.81E−03 4.20E−02 LEMD3 LEM domain containing 3 4.59E−04 1.54E−02 LILRA3 leukocyte immunoglobulin-like receptor, subfamily A 6.01E−04 1.84E−02 (without TM domain), member 3 LMBRD1 LMBR1 domain containing 1 1.82E−03 4.21E−02 LMO4 LIM domain only 4 1.07E−04 5.08E−03 LOC100093631 general transcription factor II, i; general transcription factor 1.74E−04 7.26E−03 II, i, pseudogene LOC100132062 hypothetical LOC100132062 2.07E−03 4.63E−02 LOC100288778 similar to WAS protein family homolog 1 1.53E−04 6.62E−03 LOC146880 hypothetical LOC146880 5.27E−04 1.67E−02 LOC728054 hypothetical LOC728054 1.76E−06 2.01E−04 LPCAT2/CAPNS2 lysophosphatidylcholine acyltransferase 2/calpain, small 1.01E−04 4.87E−03 subunit 2 LRMP lymphoid-restricted membrane protein 8.68E−04 2.42E−02 LRRFIP2 leucine rich repeat (in FLII) interacting protein 2 6.70E−07 9.07E−05 LRRK2 leucine-rich repeat kinase 2 2.43E−05 1.64E−03 LTA4H leukotriene A4 hydrolase 8.88E−05 4.41E−03 LY75/CD302 lymphocyte antigen 75/CD302 molecule 6.74E−18 2.01E−14 MALAT1 metastasis associated lung adenocarcinoma transcript 1 1.73E−04 7.26E−03 (non-protein coding) MAN1A1 mannosidase, alpha, class 1A, member 1 6.62E−05 3.61E−03 MAT2B methionine adenosyltransferase II, beta 1.16E−04 5.41E−03 MCL1 myeloid cell leukemia sequence 1 (BCL2-related) 2.05E−03 4.60E−02 MED4 mediator complex subunit 4 6.30E−06 5.52E−04 MEGF9 multiple EGF-like-domains 9 1.54E−03 3.77E−02 METTL9 methyltransferase like 9 7.05E−08 1.46E−05 MFSD1 major facilitator superfamily domain containing 1 2.99E−05 1.95E−03 MGST1 microsomal glutathione S-transferase 1 3.86E−05 2.33E−03 MIAT myocardial infarction associated transcript (non-protein 9.16E−08 1.70E−05 coding) MICA/HCP5 MHC class I polypeptide-related sequence A/HLA complex 2.15E−05 1.50E−03 P5 (non-protein coding) MLX MAX-like protein X 2.24E−03 4.89E−02 MMADHC methylmalonic aciduria (cobalamin deficiency) cbID type, 1.65E−04 7.08E−03 with homocystinuria MOBKL1B MOB1, Mps One Binder kinase activator-like 1B (yeast) 7.62E−11 4.25E−08 MPPE1 metallophosphoesterase 1 4.29E−13 6.39E−10 MRPL15 mitochondrial ribosomal protein L15 6.55E−04 1.96E−02 MS4A6E/MS4A7/ membrane-spanning 4-domains, subfamily A, member 1.84E−04 7.55E−03 MS4A14 6E/membrane-spanning 4-domains, subfamily A, member 7/membrane-spanning 4-domains, subfamily A, member 14 MSMB/NCOA4 microseminoprotein, beta-/nuclear receptor coactivator 4 9.13E−06 7.48E−04 MTCH1 mitochondrial carrier homolog 1 (C. elegans) 1.04E−03 2.76E−02 MTMR1 myotubularin related protein 1 7.73E−04 2.21E−02 MTMR6 myotubularin related protein 6 5.13E−04 1.67E−02 MTO1 mitochondrial translation optimization 1 homolog 3.83E−05 2.33E−03 (S. cerevisiae) MTPN/LUZP6 myotrophin/leucine zipper protein 6 5.15E−04 1.67E−02 MX1 myxovirus (influenza virus) resistance 1, interferon- 3.36E−12 3.00E−09 inducible protein p78 (mouse) MYL12A myosin, light chain 12A, regulatory, non-sarcomeric 1.66E−06 1.95E−04 MYLIP myosin regulatory light chain interacting protein 1.61E−03 3.88E−02 NAB1 NGFI-A binding protein 1 (EGR1 binding protein 1) 7.51E−05 3.95E−03 NAP1L1 nucleosome assembly protein 1-like 1 1.58E−03 3.84E−02 NAPSB napsin B aspartic peptidase pseudogene 5.81E−06 5.14E−04 NARS asparaginyl-tRNA synthetase 1.26E−04 5.70E−03 NBPF9/NOTCH2NL/ neuroblastoma breakpoint family, member 9/notch 2 N- 7.79E−04 2.21E−02 NBPF10 terminal like/neuroblastoma breakpoint family, member 10 NBR2/NBR1 neighbor of BRCA1 gene 2 (non-protein coding)/neighbor 1.77E−03 4.15E−02 of BRCA1 gene 1 NCRNA00189 long intergenic non-protein coding RNA 4.89E−06 4.50E−04 (LINC00189)/ 189/glyceraldehyde-3-phosphate dehydrogenase GAPDHP14/BACH1 pseudogene 14/BTB and CMC homology 1, basic leucine zipper transcription factor 1 NDFIP1 Nedd4 family interacting protein 1 2.26E−03 4.91E−02 NEK9 NIMA (never in mitosis gene a)- related kinase 9 2.94E−04 1.09E−02 NFE2L2 nuclear factor (erythroid-derived 2)-like 2 3.18E−04 1.14E−02 NR3C1 nuclear receptor subfamily 3, group C, member 1 3.02E−06 3.14E−04 (glucocorticoid receptor) NSUN2 NOL1/NOP2/Sun domain family, member 2 8.40E−06 7.02E−04 OAS2 2′-5′-oligoadenylate synthetase 2, 69/71 kDa 2.12E−04 8.51E−03 OAS3 2′-5′-oligoadenylate synthetase 3, 100 kDa 1.07E−03 2.84E−02 OAZ2 ornithine decarboxylase antizyme 2 7.72E−04 2.21E−02 OGFRL1 opioid growth factor receptor-like 1 4.09E−04 1.42E−02 PAFAH1B1 platelet-activating factor acetylhydrolase, isoform Ib, 4.60E−05 2.67E−03 subunit 1 (45 kDa) PAN2/CNPY2/CS PAN2 poly(A) specific ribonuclease subunit/canopy FGF 2.94E−05 1.93E−03 signaling regulator 2/citrate synthase PAPOLA poly(A) polymerase alpha 1.41E−03 3.55E−02 PARP14 poly (ADP-ribose) polymerase family, member 14 3.54E−08 7.91E−06 PARP9 poly (ADP-ribose) polymerase family, member 9 1.25E−04 5.67E−03 PCMTD2 protein-L-isoaspartate (D-aspartate) O-methyltransferase 9.19E−05 4.51E−03 domain containing 2 PDPR pyruvate dehydrogenase phosphatase regulatory subunit 3.87E−04 1.35E−02 PELI1 pellino homolog 1 (Drosophila) 2.46E−07 4.07E−05 PGK1 phosphoglycerate kinase 1 2.08E−05 1.48E−03 PHB2/SCARNA12 prohibitin 2/SCARNA12 6.25E−04 1.89E−02 PHIP/TRNAF13P pleckstrin homology domain interacting protein/transfer 2.70E−04 1.04E−02 (TRF-GAA8-1) RNA-Phe (GAA) 8-1 PJA2 praja ring finger 2 4.33E−06 4.27E−04 PLCL2 phospholipase C-like 2 1.94E−03 4.40E−02 PLDN (BLOC1S6)/ biogenesis of lysosomal organelles complex-1, subunit 6, 2.21E−03 4.84E−02 SQRDL pallidin/sulfide quinone reductase-like (yeast) PLEK pleckstrin 1.86E−09 5.93E−07 PLEKHB2 pleckstrin homology domain containing, family B (evectins) 3.65E−07 5.45E−05 member 2 PLEKHM1P pleckstrin homology domain containing, family M (with 4.23E−04 1.44E−02 RUN domain) member 1 pseudogene PNRC1 proline-rich nuclear receptor coactivator 1 1.57E−03 3.82E−02 PPIL3/CLK1 peptidylprolyl isomerase (cyclophilin)-like 3/CDC-like 5.88E−04 1.81E−02 kinase 1 PPP1CB/SPDYA protein phosphatase 1, catalytic subunit, beta 4.45E−06 4.29E−04 isozyme/speedy/RINGO cell cycle regulator family member A PPP1CC protein phosphatase 1, catalytic subunit, gamma isoform 8.17E−05 4.13E−03 PPP1R15B protein phosphatase 1, regulatory (inhibitor) subunit 15B 1.38E−03 3.50E−02 PPP2R5A protein phosphatase 2, regulatory subunit B′, alpha isoform 1.25E−07 2.24E−05 PPP3CB protein phosphatase 3 (formerly 2B), catalytic subunit, beta 2.19E−04 8.68E−03 isoform PPP3R1/WDR92 protein phosphatase 3, regulatory subunit B, alpha/WD 1.50E−06 1.79E−04 repeat domain 92 PPP4R1 protein phosphatase 4, regulatory subunit 1 5.17E−04 1.67E−02 PPP6C protein phosphatase 6, catalytic subunit 1.84E−04 7.55E−03 PPTC7 PTC7 protein phosphatase homolog (S. cerevisiae) 4.64E−05 2.67E−03 PRCP prolylcarboxypeptidase (angiotensinase C) 1.01E−03 2.72E−02 PRMT2 protein arginine methyltransferase 2 1.75E−03 4.14E−02 PRNP prion protein 5.70E−04 1.77E−02 PRPF38B PRP38 pre-mRNA processing factor 38 (yeast) domain 7.61 E−04 2.21E−02 containing B PSMA1/COPB1 proteasome (prosome, macropain) subunit, alpha type, 2.16E−03 4.76E−02 1/coatomer protein complex, subunit beta 1 PSMB3 proteasome (prosome, macropain) subunit, beta type, 3 2.03E−03 4.56E−02 PSMB8 proteasome (prosome, macropain) subunit, beta type, 8 6.21E−05 3.42E−03 (large multifunctional peptidase 7) PSMD13 proteasome (prosome, macropain) 26S subunit, non- 8.66E−07 1.14E−04 ATPase, 13 PSMD6 proteasome (prosome, macropain) 26S subunit, non- 3.66E−07 5.45E−05 ATPase, 6 PTGER4 prostaglandin E receptor 4 (subtype EP4) 6.30E−04 1.90E−02 PTPRC protein tyrosine phosphatase, receptor type, C 1.77E−23 1.59E−19 PXK PX domain containing serine/threonine kinase 2.74E−04 1.04E−02 RAB10 RAB10, member RAS oncogene family 8.67E−07 1.14E−04 RAB1A RAB1A, member RAS oncogene family 1.18E−04 5.47E−03 RAB32 RAB32, member RAS oncogene family 1.48E−03 3.67E−02 RAB6A RAB6C, member RAS oncogene family; RAB6A, member 1.20E−04 5.51E−03 RAS oncogene family; hypothetical LOC100130819; RAB6C-like RAB8B RAB8B, member RAS oncogene family 2.86E−04 1.08E−02 RAD21 RAD21 homolog (S. pombe) 2.14E−03 4.74E−02 RAF1 v-raf-1 murine leukemia viral oncogene homolog 1 4.83E−04 1.61E−02 RAP1A RAP1A, member of RAS oncogene family 4.21E−09 1.21E−06 RAP1B RAP1B, member of RAS oncogene family 3.01E−12 2.99E−09 RASSF3 Ras association (RalGDS/AF-6) domain family member 3 1.51E−03 3.70E−02 RBBP4 hypothetical LOC642954; retinoblastoma binding protein 4 9.69E−04 2.64E−02 RBL2 retinoblastoma-like 2 (p130) 4.62E−06 4.30E−04 RECQL RecQ protein-like (DMA helicase Q1-like) 4.93E−05 2.82E−03 RFWD2 ring finger and WD repeat domain 2 9.23E−06 7.50E−04 RGS18 regulator of G-protein signaling 18 8.81E−04 2.43E−02 RICTOR RPTOR independent companion of MTOR, complex 2 3.07E−08 7.22E−06 RILPL2 Rab interacting lysosomal protein-like 2 4.59E−06 4.30E−04 RIT1 Ras-like without CAAX 1 1.18E−04 5.47E−03 RNF103/VPS24 ring finger protein 103/charged multivesicular body protein 5.29E−04 1.67E−02 (CHMP3) 3 RNF13 ring finger protein 13 1.73E−08 4.30E−06 RNF141 ring finger protein 141 1.20E−05 9.15E−04 RNF145 ring finger protein 145 7.82E−09 2.06E−06 RNF213 ring finger protein 213 1.13E−10 5.60E−08 RNF31/IRF9 ring finger protein 31/interferon regulatory factor 9 2.70E−04 1.04E−02 RNF5 ring finger protein 5; ring finger protein 5 pseudogene 1 1.97E−03 4.45E−02 RNF6 ring finger protein (C3H2C3 type) 6 4.21E−04 1.44E−02 ROCK1 similar to Rho-associated, coiled-coil containing protein 1.46E−03 3.65E−02 kinase 1; Rho-associated, coiled-coil containing protein kinase 1 RPL14.1 ribosomal protein L14 1.80E−03 4.19E−02 S100A6 S100 calcium binding protein A6 1.51E−03 3.70E−02 SACM1L SAC1 suppressor of actin mutations 1-like (yeast) 5.04E−04 1.66E−02 SAR1A/TYSND1/ secretion associated, Ras related GTPase 1A/trypsin 3.26E−07 5.12E−05 AIFM2 domain containing 1/apoptosis-inducing factor, mitochondrion-associated, 2 SCP2 sterol carrier protein 2 4.97E−05 2.83E−03 SCPEP1 serine carboxypeptidase 1 8.05E−05 4.11E−03 SDHD succinate dehydrogenase complex, subunit D, integral 2.18E−03 4.80E−02 membrane protein SEC22B SEC22 vesicle trafficking protein homolog B (S. cerevisiae) 4.13E−04 1.42E−02 SEC61B Sec61 beta subunit 8.05E−05 4.11E−03 SELE/SELL selectin E/selectin L 2.96E−04 1.10E−02 SENP6 SUMO1/sentrin specific peptidase 6 1.73E−03 4.10E−02 SEPT5/GP1BB septin 5/glycoprotein Ib (platelet), beta polypeptide 1.31E−03 3.38E−02 SERINC1 serine incorporator 1 1.36E−07 2.39E−05 SERINC3 serine incorporator 3 1.02E−04 4.88E−03 SKAP2 src kinase associated phosphoprotein 2 1.03E−03 2.76E−02 SKIV2L2 superkiller viralicidic activity 2-like 2 (S. cerevisiae) 1.61E−04 6.94E−03 SLA Src-like-adaptor 3.32E−04 1.18E−02 SLBP stem-loop binding protein 1.87E−03 4.29E−02 SLC12A7 solute carrier family 12 (potassium/chloride transporters), 2.26E−03 4.91E−02 member 7 SLC25A37 solute carrier family 25, member 37 9.13E−05 4.51E−03 SLK STE20-like kinase (yeast) 1.49E−04 6.55E−03 SLU7 SLU7 splicing factor homolog (S. cerevisiae) 8.40E−04 2.36E−02 SMAP2 small ArfGAP2 1.92E−03 4.35E−02 SMARCA5 SWI/SNF related, matrix associated, actin dependent 9.51E−04 2.60E−02 regulator of chromatin, subfamily a, member 5 SMCHD1 structural maintenance of chromosomes flexible hinge 2.21E−10 9.86E−08 domain containing 1 SNX10 sorting nexin 10 1.40E−06 1.71E−04 SNX14 sorting nexin 14 2.09E−06 2.30E−04 SNX2 sorting nexin 2 1.60E−03 3.88E−02 SNX6 sorting nexin 6 3.38E−05 2.16E−03 SP140L/SP100/ SP140 nuclear body protein-like/SP100 nuclear 1.69E−04 7.17E−03 HMGB1L3 antigen/high mobility group box 1 pseudogene 3 SPATA13/C1QTNF9 spermatogenesis associated 13/C1q and tumor necrosis 1.80E−06 2.01E−04 factor related protein 9 SPCS3 signal peptidase complex subunit 3 homolog 4.54E−06 4.30E−04 (S. cerevisiae) SPOPL speckle-type POZ protein-like 8.45E−10 3.02E−07 SPPL2A signal peptide peptidase-like 2A 3.22E−05 2.08E−03 SRI sorcin 3.49E−06 3.54E−04 SRP9/EPHX1 signal recognition particle 9 kDa/epoxide hydrolase 1, 7.37E−08 1.50E−05 microsomal (xenobiotic) SSFA2 sperm specific antigen 2 9.73E−04 2.64E−02 ST8SIA4 ST8 alpha-N-acetyl-neuraminide alpha-2,8- 1.14E−03 3.00E−02 sialyltransferase 4 STAT1 signal transducer and activator of transcription 1, 91 kDa 8.77E−04 2.43E−02 STOM stomatin 4.35E−05 2.56E−03 STXBP3 syntaxin binding protein 3 1.24E−06 1.56E−04 SURF4 surfeit 4 1.20E−03 3.15E−02 SYTL2 synaptotagmin-like 2 9.74E−04 2.64E−02 TAF1 TAF1 RNA polymerase II, TATA box binding protein (TBP)- 4.42E−04 1.49E−02 associated factor, 250 kDa TAGAP T-cell activation RhoGTPase activating protein 1.01E−04 4.87E−03 TAX1BP1 Tax1 (human T-cell leukemia virus type I) binding protein 1 1.91E−05 1.36E−03 TBC1D2B TBC1 domain family, member 2B 6.79E−05 3.66E−03 TCF25/MC1R/ transcription factor 25 (basic helix-loop-helix)/melanocortin 2.12E−09 6.52E−07 TUBB3 1 receptor (alpha melanocyte stimulating hormone receptor)/tubulin, beta 3 class III TCP11L2 t-complex 11 (mouse)-like 2 3.73E−04 1.31E−02 TDG similar to G/T mismatch-specific thymine DMA glycosylase; 1.87E−03 4.29E−02 thymine-DNA glycosylase TDP2 tyrosyl-DNA phosphodiesterase 2 1.70E−03 4.07E−02 TES testis derived transcript (3 LIM domains) 2.74E−04 1.04E−02 TGFBR2 transforming growth factor, beta receptor II (70/80 kDa) 1.05E−04 4.97E−03 TM9SF2 transmembrane 9 superfamily member 2 2.95E−10 1.25E−07 TM9SF3 transmembrane 9 superfamily member 3 1.74E−04 7.26E−03 TMCC1 transmembrane and coiled-coil domain family 1 2.13E−04 8.52E−03 TMCO3 transmembrane and coiled-coil domains 3 7.11E−05 3.78E−03 TMEM167B transmembrane protein 167B 2.78E−05 1.85E−03 TMEM222 transmembrane protein 222 1.41E−04 6.27E−03 TMEM49 transmembrane protein 49 5.38E−06 4.86E−04 TMEM59 transmembrane protein 59 8.49E−05 4.26E−03 TMSB4X thymosin-like 2 (pseudogene); thymosin-like 1 6.06E−04 1.85E−02 (pseudogene); thymosin beta 4, X-linked TNFSF13B tumor necrosis factor (ligand) superfamily, member 13b 3.47E−04 1.23E−02 TNKS2 tankyrase, TRF1-interacting ankyrin-related ADP-ribose 8.73E−04 2.42E−02 polymerase 2 TNPO3 transportin 3 4.02E−05 2.41E−03 TOPORS/DDX58 topoisomerase I binding, arginine/serine-rich, E3 ubiquitin 6.89E−04 2.03E−02 protein ligase/DEAD (Asp-Glu-Ala-Asp) box polypeptide 58 TOR1A torsin family 1, member A (torsin A) 1.11E−07 2.02E−05 TOR1AIP1 torsin A interacting protein 1 5.49E−04 1.73E−02 TPM3 tropomyosin 3 4.32E−07 6.23E−05 TRAM1 translocation associated membrane protein 1 1.79E−06 2.01E−04 TRPC4AP transient receptor potential cation channel, subfamily C, 1.30E−05 9.81E−04 member 4 associated protein TSNAX/DISC1 translin-associated factor X/disrupted in schizophrenia 1 4.89E−04 1.62E−02 TSPAN14 tetraspanin 14 1.16E−05 8.98E−04 TXNRD1 thioredoxin reductase 1; hypothetical LOC100130902 8.52E−08 1.65E−05 U2AF1 U2 small nuclear RNA auxiliary factor 1 3.82E−05 2.33E−03 UBE2B ubiquitin-conjugating enzyme E2B (RAD6 homolog) 2.65E−04 1.02E−02 UBE2E3 ubiquitin-conjugating enzyme E2E 3 (UBC4/5 homolog, 6.50E−04 1.95E−02 yeast) UBL7 ubiquitin-like 7 (bone marrow stromal cell-derived) 2.09E−03 4.66E−02 UBR2 ubiquitin protein ligase E3 component n-recognin 2 7.78E−04 2.21E−02 UHMK1 U2AF homology motif (UHM) kinase 1 1.28E−03 3.32E−02 USP1 ubiquitin specific peptidase 1 1.36E−03 3.47E−02 USP15 ubiquitin specific peptidase 15 2.60E−05 1.75E−03 USP33 ubiquitin specific peptidase 33 7.17E−04 2.09E−02 UTRN utrophin 5.40E−15 9.66E−12 VAMP3 vesicle-associated membrane protein 3 (cellubrevin) 1.62E−04 6.94E−03 VCP valosin-containing protein 6.72E−04 2.00E−02 VNN2 vanin 2 1.49E−03 3.69E−02 VPS13C vacuolar protein sorting 13 homolog C (S. cerevisiae) 3.31E−04 1.18E−02 WARS tryptophanyl-tRNA synthetase 1.44E−04 6.37E−03 WDFY2 WD repeat and FYVE domain containing 2 1.87E−03 4.29E−02 WSB1 WD repeat and SOCS box-containing 1 1.39E−04 6.20E−03 yakeme 5.07E−04 1.66E−02 YIPF4 Yip1 domain family, member 4 2.65E−04 1.02E−02 YWHAE similar to 14-3-3 protein epsilon (14-3-3E) (Mitochondrial 9.45E−10 3.13E−07 import stimulation factor L subunit) (MSF L); tyrosine 3- monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide ZBED5/EIF4G2/ zinc finger, BED-type containing 5/eukaryotic translation 4.27E−04 1.45E−02 SNORD97 initiation factor 4 gamma, 2/small nucleolar RNA, C/D box 97 ZCCHC6 zinc finger, CCHC domain containing 6 3.66E−05 2.26E−03 ZEB2/GTDC1 zinc finger E-box binding homeobox 2/glycosyltransferase- 1.36E−04 6.12E−03 like domain containing 1 ZFAND5 zinc finger, AN1-type domain 5 2.10E−05 1.48E−03 ZFP91-CNTF zinc finger protein 91 homolog (mouse); ZFP91-CNTF 9.98E−06 8.03E−04 readthrough transcript; ciliary neurotrophic factor ZNF516 zinc finger protein 516 2.98E−04 1.10E−02 ZNF592 zinc finger protein 592 1.35E−03 3.45E−02

TABLE 5 Canonical Pathways of the 412 Genes with Differential Alternative Splicing Among Large Vessel Ischemic Stroke (IS), Cardioembolic IS, Lacunar IS, Intracerebral Hemorrhage and Controls. B-H-Benjamini-Hochberg corrected p-value Ingenuity Canonical -log(p- -log(B-H Pathways value) p-value) Ratio Molecules CD28 Signaling in T 8.11E00 5.54E00 1.36E−01 CDC42, ACTR2, CALM1 (includes others), ARPC3, Helper Cells HLA-DQA1, ATM, PPP3CB, ARPC5L, ACTR3, HLA-DRB1, PPP3R1, HLA-DMA, ARPC4, HLA-DMB, PTPRC, CD86 Cdc42 Signaling 5.99E00 3.72E00 9.58E−02 CDC42, ACTR2, ARPC3, HLA-DQA1, RAF1, CDC42SE1, MYL12A, ARPC5L, ACTR3, HLA-DRB1, HLA-DMA, ARPC4, HLA-DMB, PPP1CB, ITGA4, IQGAP2 Nur77 Signaling in T 5.38E00 3.33E00 1.58E−01 HLA-DRB1, CALM1 (includes others), PPP3R1, APAF1, Lymphocytes HLA-DMA, HLA-DQA1, HLA-DMB, PPP3CB, CD86 fMLP Signaling in  5.3E00 3.33E00 1.11E−01 CDC42, ACTR2, CALM1 (includes others), PPP3R1, Neutrophils ARPC3, RAF1, ARPC4, ATM, PPP3CB, ARPC5L, CYBB, ACTR3 Interferon Signaling 4.92E00 3.04E00 1.94E−01 IFNGR1, IRF9, JAK2, STAT1, MX1, IFNAR1, PSMB8 Rac Signaling  4.7E00 2.91E00 1.06E−01 CDC42, ACTR2, ARPC3, RAF1, ARPC4, ATM, ITGA4, IQGAP2, ARPC5L, CYBB, ACTR3 Actin Nucleation by 4.51E00 2.83E00 1.43E−01 CDC42, ACTR2, ARPC3, ARPC4, ROCK1, ITGA4, ARP-WASP Complex ARPC5L, ACTR3 Regulation of Actin- 4.47E00 2.83E00  1.1E−01 CDC42, ACTR2, ARPC3, ARPC4, MYL12A, PPP1CB, based Motility by Rho ROCK1, ITGA4, ARPC5L, ACTR3 Ephrin Receptor 4.45E00 2.83E00 8.05E−02 CDC42, ACTR2, JAK2, ARPC3, EPHB4, CRKL, RAF1, Signaling ARPC5L, RAP1A, ACTR3, ARPC4, RAP1B, ROCK1, ITGA4 Integrin Signaling 4.32E00 2.75E00 7.43E−02 CDC42, ACTR2, ARPC3, CRKL, RAF1, ATM, MYL12A, ARPC5L, RAP1A, ACTR3, ARPC4, RAP1B, PPP1CB, ROCK1, ITGA4 Protein Kinase A 4.28E00 2.75E00 5.73E−02 ANAPC13, PPP1CC, TDP2, CALM1 (includes others), MPPE1, Signaling ADCY7, RAF1, AKAP8, MYL12A, H3F3A/H3F3B, PPP3CB, YWHAE, RAP1A, ADD3, TGFBR2, PPP3R1, RAP1B, PPP1CB, ROCK1, PLCL2, PTPRC, ANAPC7 B Cell Development 4.04E00 2.54E00 1.76E−01 HLA-DRB1, HLA-DMA, HLA-DQA1, HLA-DMB, PTPRC, CD86 Actin Cytoskeleton 3.97E00 2.51E00 6.91E−02 CDC42, ACTR2, ARPC3, CRKL, RAF1, ATM, MYL12A, ARPC5L, Signaling ACTR3, ARPC4, PPP1CB, ROCK1, ITGA4, IQGAP2, TMSB10/TMSB4X Antigen Presentation 3.83E00  2.4E00 1.62E−01 HLA-DRB1, CD74, HLA-DMA, HLA-DQA1, HLA-DMB, PSMB8 Pathway Role of JAK1, JAK2 and  3.8E00  2.4E00 2.08E−01 IFNGR1, JAK2, STAT1, RAF1, IFNAR1 TYK2 in Interferon Signaling T Helper Cell 3.76E00 2.39E00 1.13E−01 IFNGR1, TGFBR2, HLA-DRB1, HLA-DMA, HLA-DQA1, STAT1, Differentiation HLA-DMB, CD86 Calcium-induced T 3.28E00 1.96E00 1.09E−01 HLA-DRB1, CALM1 (includes others), PPP3R1, HLA-DMA, Lymphocyte Apoptosis HLA-DQA1, HLA-DMB, PPP3CB Retinoic acid 3.28E00 1.96E00 1.09E−01 CFLAR, APAF1, TNKS2, PARP9, PARP14, DAP3, IFNAR1 Mediated Apoptosis Signaling iCOS-iCOSL Signaling in 3.17E00  1.9E00 8.33E−02 HLA-DRB1, CALM1 (includes others), PPP3R1, HLA-DMA, T Helper Cells HLA-DQA1, ATM, HLA-DMB, PPP3CB, PTPRC Dendritic Cell 3.17E00  1.9E00  6.7E−02 HLA-DRB1, JAK2, HLA-DMA, HLA-DQA1, CD58, STAT1, ATM, Maturation HLA-DMB, PLCL2, LY75, CD86, IFNAR1 NRF2-mediated 3.15E00  1.9E00 6.67E−02 GSTO1, BACH1, RAF1, ATM, UBE2E3, TXNRD1, EPHX1, Oxidative Stress DNAJB6, VCP, GSTK1, MGST1, NFE2L2 Response Type I Diabetes 3.11E00 1.88E00 8.18E−02 IFNGR1, HLA-DRB1, APAF1, JAK2, HLA-DMA, HLA-DQA1, Mellitus Signaling STAT1, HLA-DMB, CD86 IL-3 Signaling 3.01E00 1.81E00 9.86E−02 PPP3R1, JAK2, CRKL, STAT1, RAF1, ATM, PPP3CB ERK/MAPK Signaling   3E00 1.81E00 6.42E−02 PPP1CC, PPP2R5A, CRKL, STAT1, RAF1, ATM, RAP1B, H3F3A/H3F3B, PPP1CB, ITGA4, RAP1A, PPP2CA Breast Cancer 2.92E00 1.75E00 6.28E−02 PPP1CC, CDC42, CALM1 (includes others), UHMK1, Regulation by PPP2R5A, TUBB3, ADCY7, RAF1, ATM, PPP1CB, ROCK1, Stathmin1 PPP2CA Synaptic Long Term 2.87E00 1.71E00 7.56E−02 PPP1CC, CALM1 (includes others), PPP3R1, RAF1, Potentiation RAP1B, PPP3CB, PPP1CB, PLCL2, RAP1A Ascorbate Recycling 2.84E00 1.71E00 6.67E−01 GSTO1, GLRX (Cytosolic) IL-4 Signaling 2.83E00 1.71E00 9.21E−02 HLA-DRB1, JAK2, HLA-DMA, HLA-DQA1, NR3C1, ATM, HLA-DMB Role of NFAT in 2.81E00 1.71E00 6.43E−02 HLA-DRB1, CALM1 (includes others), PPP3R1, HLA-DMA, Regulation of the HLA-DQA1, RAF1, ATM, HLA-DMB, PPP3CB, FCER1A, CD86 Immune Response Epithelial Adherens  2.8E00 1.71E00 6.85E−02 TGFBR2, CDC42, ACTR2, ARPC3, TUBB3, ARPC4, RAP1B, Junction Signaling ARPC5L, RAP1A, ACTR3 RhoA Signaling 2.79E00 1.71E00 7.38E−02 ACTR2, ARPC3, ARPC4, MYL12A, PPP1CB, ROCK1, ARPC5L, ACTR3, SEPT5 Signaling by Rho 2.64E00 1.57E00 5.56E−02 CDC42, ACTR2, ARPC3, RAF1, ATM, MYL12A, ARPC5L, Family GTPases ACTR3, SEPT5, ARPC4, ROCK1, ITGA4, CYBB Production of Nitric 2.63E00 1.57E00 6.11E−02 PPP1CC, IFNGR1, JAK2, PPP2R5A, STAT1, ATM, RAP1B, Oxide and Reactive PPP1CB, CYBB, RAP1A, PPP2CA Oxygen Species in Macrophages GM-CSF Signaling 2.61E00 1.56E00 9.68E−02 PPP3R1, JAK2, STAT1, RAF1, ATM, PPP3CB Leukotriene 2.48E00 1.47E00 2.14E−01 DPEP3, DPEP2, LTA4H Biosynthesis Vitamin-C Transport 2.48E00 1.47E00 2.14E−01 GSTO1, GLRX, TXNRD1 Mitotic Roles of Polo- 2.47E00 1.47E00 9.09E−02 SLK, ANAPC13, RAD21, PPP2R5A, ANAPC7, PPP2CA Like Kinase CTLA4 Signaling in 2.47E00 1.47E00 7.95E−02 JAK2, PPP2R5A, CLTC, ATM, AP1S2, CD86, PPP2CA Cytotoxic T Lymphocytes cAMP-mediated 2.43E00 1.45E00 5.48E−02 RGS18, TDP2, CALM1 (includes others), PPP3R1, signaling ADCY7, MPPE1, RAF1, AKAP8, PPP3CB, PTGER4, RAP1A, MC1R Axonal Guidance 2.41E00 1.44E00 4.39E−02 CDC42, ACTR2, ARPC3, EPHB4, TUBB3, CRKL, RAF1, Signaling ATM, MYL12A, PPP3CB, ARPC5L, RAP1A, ACTR3, PPP3R1, ARPC4, RAP1B, ROCK1, ITGA4, PLCL2 Remodeling of  2.4E00 1.44E00 8.82E−02 ACTR2, ARPC3, TUBB3, ARPC4, ARPC5L, ACTR3 Epithelial Adherens Junctions Graft-versus-Host 2.39E00 1.43E00 1.04E−01 HLA-DRB1, HLA-DMA, HLA-DQA1, HLA-DMB, CD86 Disease Signaling Autoimmune Thyroid 2.35E00 1.41E00 1.02E−01 HLA-DRB1, HLA-DMA, HLA-DQA1, HLA-DMB, CD86 Disease Signaling Fcγ Receptor- 2.33E00  1.4E00 7.53E−02 CDC42, ACTR2, VAMP3, ARPC3, ARPC4, ARPC5L, ACTR3 mediated Phagocytosis in Macrophages and Monocytes Protein Ubiquitination 2.32E00  1.4E00  5.1E−02 UBR2, UBE2E3, PSMD6, USP1, USP15, UBE2B, PSMD13, Pathway DNAJB6, PSMB3, PAN2, PSMA1, USP33, PSMB8 PKCθ Signaling in T 2.32E00  1.4E00 6.78E−02 HLA-DRB1, PPP3R1, HLA-DMA, HLA-DQA1, ATM, HLA-DMB, Lymphocytes PPP3CB, CD86 Glucocorticoid 2.24E00 1.34E00 4.98E−02 JAK2, RAF1, ATM, PPP3CB, SELE, ANXA1, TGFBR2, Receptor Signaling HMGB1, PPP3R1, NR3C1, STAT1, CDKN1C, TAF1 Glutathione Redox 2.16E00 1.27E00 1.67E−01 GPX1, GSTK1, MGST1 Reactions I PDGF Signaling 2.14E00 1.27E00 7.79E−02 EIF2AK2, JAK2, CRKL, STAT1, RAF1, ATM Role of Pattern 2.13E00 1.27E00  6.3E−02 EIF2AK2, EIF2S1, IFIH1, OAS3, ATM, OAS2, DDX58, Recognition Receptors CLEC7A in Recognition of Bacteria and Viruses D-myo-inositol 2.13E00 1.27E00  6.3E−02 PPP1CC, PPTC7, PPP2R5A, PPP4R1, SACM1L, IPMK, (1,4,5,6)- PTPRC, MTMR6 Tetrakisphosphate Biosynthesis D-myo-inositol 2.13E00 1.27E00  6.3E−02 PPP1CC, PPTC7, PPP2R5A, PPP4R1, SACM1L, IPMK, (3,4,5,6)- PTPRC, MTMR6 tetrakisphosphate Biosynthesis Clathrin-mediated 2.07E00 1.22E00 5.41E−02 CDC42, ACTR2, PPP3R1, ARPC3, CLTC, ARPC4, ATM, Endocytosis Signaling PPP3CB, ARPC5L, ACTR3 HGF Signaling 2.05E00 1.21E00 6.67E−02 CDC42, CRKL, RAF1, ATM, RAP1B, ITGA4, RAP1A Cardiac β-adrenergic 2.01E00 1.18E00 6.02E−02 PPP1CC, TDP2, PPP2R5A, ADCY7, MPPE1, AKAP8, Signaling PPP1CB, PPP2CA Dopamine-DARPP32   2E00 1.18E00 5.59E−02 PPP1CC, CALM1 (includes others), PPP3R1, PPP2R5A, Feedback in cAMP ADCY7, PPP3CB, PPP1CB, PLCL2, PPP2CA Signaling Cardiac Hypertrophy 1.95E00 1.13E00 4.93E−02 TGFBR2, CALM1 (includes others), PPP3R1, ADCY7, Signaling RAF1, ATM, MYL12A, PPP3CB, ROCK1, PLCL2, ADSS Role of PKR in 1.93E00 1.12E00   1E−01 EIF2AK2, EIF2S1, APAF1, STAT1 Interferon Induction and Antiviral Response HIPPO signaling 1.91E00 1.11E00 6.98E−02 PPP1CC, PPP2R5A, MOB1A, PPP1CB, YWHAE, PPP2CA Salvage Pathways of  1.9E00  1.1E00  2.5E−01 APOBEC3B, APOBEC3A Pyrimidine Deoxyribonucleotides Altered T Cell and B 1.87E00 1.09E00 6.82E−02 TNFSF13B, HLA-DRB1, HLA-DMA, HLA-DQA1, HLA-DMB, Cell Signaling in CD86 Rheumatoid Arthritis UVA-Induced MAPK 1.87E00 1.09E00 6.82E−02 STAT1, ATM, TNKS2, PARP9, PLCL2, PARP14 Signaling Activation of IRF by 1.86E00 1.09E00 7.81E−02 IRF9, STAT1, IFIH1, DDX58, IFNAR1 Cytosolic Pattern Recognition Receptors 3-phosphoinositide 1.82E00 1.05E00 5.56E−02 PPP1CC, MTMR1, PPTC7, PPP2R5A, PPP4R1, SACM1L, Degradation PTPRC, MTMR6 RhoGDI Signaling 1.81E00 1.05E00  5.2E−02 CDC42, ACTR2, ARPC3, ARPC4, MYL12A, ROCK1, ITGA4, ARPC5L, ACTR3 iNOS Signaling 1.79E00 1.04E00 9.09E−02 IFNGR1, CALM1 (includes others), JAK2, STAT1 Death Receptor 1.78E00 1.03E00 6.52E−02 CFLAR, APAF1, TNKS2, ROCK1, PARP9, PARP14 Signaling B Cell Receptor 1.77E00 1.03E00 5.11E−02 CDC42, CALM1 (includes others), PPP3R1, RAF1, ATM, Signaling RAP1B, PPP3CB, PTPRC, RAP1A PI3K/AKT Signaling  1.7E00  9.65E−01 5.69E−02 JAK2, PPP2R5A, MCL1, RAF1, ITGA4, YWHAE, PPP2CA T Cell Receptor 1.68E00  9.48E−01 6.19E−02 CALM1 (includes others), PPP3R1, RAF1, ATM, Signaling PPP3CB, PTPRC Histamine 1.65E00  9.38E−01  1E00 HDC Biosynthesis UDP-N-acetyl-D- 1.65E00  9.38E−01  1E00 GALE galactosamine Biosynthesis I 3-phosphoinositide 1.65E00  9.38E−01 5.16E−02 PPP1CC, PPTC7, PPP2R5A, PPP4R1, ATM, SACM1L, Biosynthesis PTPRC, MTMR6 CDK5 Signaling 1.64E00  9.38E−01 6.06E−02 PPP1CC, PPP2R5A, ADCY7, RAF1, PPP1CB, PPP2CA Prolactin Signaling 1.64E00  9.38E−01 6.85E−02 JAK2, STAT1, NR3C1, RAF1, ATM Glutathione-mediated 1.63E00  9.34E−01 1.07E−01 GSTO1, GSTK1, MGST1 Detoxification Superpathway of 1.55E00  8.69E−01 4.69E−02 PPP1CC, PPTC7, PPP2R5A, PPP4R1, ATM, SACM1L, Inositol Phosphate IPMK, PTPRC, MTMR6 Compounds CNTF Signaling 1.55E00  8.69E−01 7.69E−02 JAK2, STAT1, RAF1, ATM Dopamine Receptor 1.53E00  8.51E−01 6.41E−02 PPP1CC, PPP2R5A, ADCY7, PPP1CB, PPP2CA Signaling Pancreatic 1.51E00  8.41E−01 5.66E−02 TGFBR2, CDC42, JAK2, STAT1, RAF1, ATM Adenocarcinoma Signaling Regulation of IL-2 1.51E00  8.41E−01 6.33E−02 TGFBR2, CALM1 (includes others), PPP3R1, RAF1, Expression in PPP3CB Activated and Anergic T Lymphocytes NGF Signaling 1.49E00  8.34E−01 5.61E−02 CDC42, RAF1, ATM, RAP1B, ROCK1, RAP1A Thrombopoietin 1.47E00  8.18E−01 7.27E−02 JAK2, STAT1, RAF1, ATM Signaling Aryl Hydrocarbon 1.43E00  7.84E−01   5E−02 GSTO1, APAF1, RBL2, ATM, GSTK1, MGST1, NFE2L2 Receptor Signaling Oncostatin M 1.41E00  7.68E−01 8.82E−02 JAK2, STAT1, RAF1 Signaling Inhibition of 1.41E00  7.68E−01 8.82E−02 CD47, TGFBR2, CD36 Angiogenesis by TSP1 D-myo-inositol-5- 1.39E00  7.6E−01  4.9E−02 PPP1CC, PPTC7, PPP2R5A, PPP4R1, SACM1L, PTPRC, MTMR6 phosphate Metabolism Phospholipase C 1.38E00  7.6E−01 4.18E−02 CALM1 (includes others), PPP3R1, ADCY7, RAF1, Signaling MYL12A, RAP1B, PPP3CB, PPP1CB, ITGA4, RAP1A Cell Cycle Regulation 1.38E00  7.6E−01 8.57E−02 PPP2R5A, CNOT7, PPP2CA by BTG Family Proteins Allograft Rejection 1.37E00  7.6E−01 5.81E−02 HLA-DRB1, HLA-DMA, HLA-DQA1, HLA-DMB, CD86 Signaling Telomere Extension by 1.37E00  7.6E−01 1.33E−01 TNKS2, HNRNPA2B1 Telomerase Spliceosomal Cycle 1.36E00  7.6E−01   5E−01 LOC102724594/U2AF1 S-methyl-5-thio-α-D- 1.36E00  7.6E−01   5E−01 APIP ribose 1-phosphate Degradation Glutamate 1.36E00  7.6E−01   5E−01 GLUD1 Biosynthesis II Glutamate 1.36E00  7.6E−01   5E−01 GLUD1 Degradation X Regulation of eIF4 and 1.35E00  7.59E−01 4.79E−02 EIF2S1, PPP2R5A, RAF1, ATM, ITGA4, EIF4G2, p70S6K Signaling PPP2CA Calcium Signaling 1.34E00  7.57E−01 4.49E−02 TPM3, ATP2B4, CALM1 (includes others), PPP3R1, RAP1B, PPP3CB, MICU1, RAP1A Gαq Signaling 1.34E00  7.57E−01 4.76E−02 RGS18, CALM1 (includes others), PPP3R1, RAF1, ATM, PPP3CB, ROCK1 RANK Signaling in 1.34E00  7.57E−01 5.68E−02 CALM1 (includes others), PPP3R1, RAF1, ATM, PPP3CB Osteoclasts Role of NFAT in 1.33E00  7.56E−01 4.47E−02 TGFBR2, CALM1 (includes others), PPP3R1, ADCY7, Cardiac Hypertrophy RAF1, ATM, PPP3CB, PLCL2 PAK Signaling 1.32E00  7.48E−01 5.62E−02 CDC42, RAF1, ATM, MYL12A, ITGA4 p70S6K Signaling 1.31E00  7.39E−01 5.04E−02 PPP2R5A, RAF1, ATM, PLCL2, YWHAE, PPP2CA

TABLE 6 Functions, Associated with the Top 2 Molecular and Cellular Functions Over-Represented in the 412 Differentially Aternatively Spliced Genes - Cell Death and Survival, and Cell-to-Cell Signaling Diseases or Categories Functions Annotation p-Value Molecules # Molecules Cell Death and cell death 1.32E−09 ACSL4, AIFM2, AKAP8, ANXA1, ANXA7, APAF1, APH1A, APIP, 148 Survival APOBEC3B, ARL6IP5, ARNTL, ATM, ATP2B4, ATP6V1G2, BAZ1A, BRAT1, C1QTNF9, CALM1 (includes others), CARD8, CCAR1, CCT8, CD164, CD244, CD36, CD46, CD47, CD53, CD74, CD86, CDC42, CDKN1C, CFLAR, CHMP3, CNPY2, CTSS, CYBB, CYLD, DAP3, DDX19A, DDX3X, DDX58, DNAJB6, DPYD, DUSP22, EGLN1, EIF2AK2, EIF2S1, EIF4G2, EPHB4, EPHX1, ERN1, FCER1A, FKBP1A, FNTA, GLRX, GLUD1, GMCL1, GPX1, GZMA, HEXB, HIPK3, HLA-DMA, HLA-DRB1, HMGB1, IFIH1, IFNAR1, IFNGR1, IFRD1, IGFBP7, ING4, IPMK, IQGAP2, ITGA4, JAK2, KLF13, LMO4, LRRK2, MC1R, MCL1, MICA, MOB1A, MTCH1, MTMR6, MTPN, MX1, NCOA4, NFE2L2, NR3C1, OAS3, PAFAH1B1, PARP14, PHB2, PHIP, PPP1CC, PPP1R15B, PPP2CA, PPP2R5A, PPP3CB, PPP3R1, PRMT2, PRNP, PSMB8, PSMD6, PTGER4, PTPRC, RAB1A, RAB32, RAD21, RAF1, RAP1A, RAP1B, RASSF3, RBBP4, RBL2, RECQL, RFWD2, RICTOR, RIT1, RNF13, RNF31, RNF5, ROCK1, S100A6, SCP2, SELL, SERINC3, SLC12A7, SLK, SMARCA5, SRI, ST8SIA4, STAT1, TAX1BP1, TDP2, TGFBR2, TMSB10/TMSB4X, TNFSF13B, TNKS2, TOPORS, TPM3, TUBB3, TXNRD1, UBE2B, VAMP3, VCP, YWHAE, ZEB2, ZFAND5 Cell Death and apoptosis 4.11E−09 ACSL4, AIFM2, AKAP8, ANXA1, ANXA7, APAF1, APH1A, APIP, APOBEC3B, ARL6IP5, ATM, ATP2B4, ATP6V1G2, BAZ1A, 122 Survival BRAT1, C1QTNF9, CARD8, CCAR1, CD164, CD36, CD47, CD53, CD74, CDC42, CDKN1C, CFLAR, CTSS, CYBB, CYLD, DAP3, DDX19A, DDX3X, DDX58, DUSP22, EIF2AK2, EIF2S1, EIF4G2, EPHB4, EPHX1, ERN1, FCER1A, FKBP1A, FNTA, GLRX, GLUD1, GMCL1, GPX1, GZMA, HEXB, HIPK3, HLA-DMA, HMGB1, IFIH1, IFNAR1, IFNGR1, IGFBP7, ING4, IQGAP2, ITGA4, JAK2, KLF13, LMO4, LRRK2, MC1R, MCL1, MOB1A, MTCH1, MTMR6, MTPN, MX1, NCOA4, NFE2L2, NR3C1, OAS3, PAFAH1B1, PARP14, PHB2, PHIP, PPP1CC, PPP2CA, PPP3CB, PPP3R1, PRMT2, PRNP, PSMB8, PSMD6, PTGER4, PTPRC, RAB32, RAD21, RAF1, RAP1A, RAP1B, RASSF3, RBBP4, RBL2, RFWD2, RICTOR, RIT1, RNF13, RNF31, RNF5, ROCK1, S100A6, SELL, SERINC3, SLK, SRI, ST8SIA4, STAT1, TAX1BP1, TDP2, TGFBR2, TMSB10/TMSB4X, TNFSF13B, TOPORS, TXNRD1, UBE2B, VCP, YWHAE, ZEB2, ZFAND5 Cell Death and necrosis 6.80E−05 ANXA1, APAF1, APIP, APOBEC3B, ATM, ATP2B4, ATP6V1G2, BAZ1A, BRAT1, C1QTNF9, CARD8, CCAR1, CCT8, CD36, 106 Survival CD47, CD74, CD86, CDC42, CDKN1C, CFLAR, CNPY2, CTSS, CYBB, CYLD, DAP3, DDX3X, DDX58, DPYD, EGLN1, EIF2AK2, EIF2S1, EIF4G2, EPHB4, EPHX1, ERN1, FCER1A, FKBP1A, FNTA, GLRX, GLUD1, GPX1, GZMA, HLA-DMA, HMGB1, IFIH1, IFNAR1, IFNGR1, IFRD1, IGFBP7, IPMK, IQGAP2, ITGA4, JAK2, KLF13, LMO4, LRRK2, MC1R, MCL1, MTMR6, MTPN, MX1, NFE2L2, NR3C1, OAS3, PAFAH1B1, PARP14, PHIP, PPP1CC, PPP2CA, PPP3CB, PPP3R1, PRMT2, PRNP, PSMB8, PSMD6, PTGER4, PTPRC, RAB32, RAD21, RAF1, RASSF3, RBBP4, RBL2, RECQL, RFWD2, RICTOR, RIT1, RNF13, RNF31, RNF5, ROCK1, S100A6, SCP2, SELL, SLK, SRI, STAT1, TAX1BP1, TDP2, TGFBR2, TMSB10/TMSB4X, TNFSF13B, TUBB3, TXNRD1, VCP, YWHAE Cell Death and cell viability 2.26E−04 APAF1, APOBEC3A, ATM, C1QTNF9, CD47, CD74, CD86, CDC42, CDKL3, CDKN1C, CFLAR, CYBB, CYLD, DPYD, DUSP22, 59 Survival EPHB4, ERN1, FCER1A, GLUD1, GPX1, HMGB1, IFIH1, IGFBP7, IRF9, JAK2, LRRK2, MCL1, MGST1, MTMR1, MTMR6, MX1, NFE2L2, NR3C1, PARP14, PPP1CB, PPP1CC, PPP2CA, PPP2R5A, PPP4R1, PPP6C, PRNP, PSMA1, PTPRC, RAD21, RAF1, RBBP4, RICTOR, RIT1, RNF31, S100A6, SELE, SELL, SPDYA, STAT1, TDP2, TGFBR2, TNFSF13B, TUBB3, VCP Cell Death and fragmentation 3.36E−04 APAF1, APOBEC3B, CD53, EIF2AK2, GPX1, GZMA, MCL1, MTCH1, NR3C1, PPP1CC, PRNP, SERINC3, STAT1 13 Survival, DNA of DNA Replication, Recombination, and Repair Cell Death and cell death of 3.43E−04 APAF1, ATM, BAZ1A, BRAT1, CARD8, CCAR1, CCT8, CD47, CDC42, CDKN1C, CFLAR, CNPY2, CYLD, DAP3, DDX3X, DDX58, 67 Survival tumor cell lines DPYD, EGLN1, EIF2AK2, EIF2S1, EIF4G2, EPHB4, ERN1, FCER1A, FKBP1A, GLRX, GPX1, IFNAR1, IFRD1, IGFBP7, IPMK, IQGAP2, ITGA4, JAK2, LMO4, MCL1, MTMR6, NFE2L2, NR3C1, OAS3, PARP14, PHIP, PPP2CA, PRNP, PTPRC, RAB32, RAD21, RAF1, RASSF3, RBL2, RFWD2, RICTOR, RIT1, RNF13, RNF31, RNF5, S100A6, SRI, STAT1, TDP2, TGFBR2, TMSB10/TMSB4X, TNFSF13B, TUBB3, TXNRD1, VCP, YWHAE Cell Death and cell survival 3.95E−04 APAF1, APOBEC3A, ATM, C1QTNF9, CD47, CD74, CD86, CDC42, CDKL3, CDKN1C, CFLAR, CYBB, CYLD, DDX3X, DPYD, 62 Survival DUSP22, EIF2S1, EPHB4, ERN1, FCER1A, GLRX, GLUD1, GPX1, HMGB1, IFIH1, IGFBP7, IRF9, JAK2, LRRK2, MCL1, MGST1, MTMR1, MTMR6, MX1, NFE2L2, NR3C1, PARP14, PPP1CB, PPP1CC, PPP2CA, PPP2R5A, PPP4R1, PPP6C, PRNP, PSMA1, PTPRC, RAD21, RAF1, RBBP4, RICTOR, RIT1, RNF31, S100A6, SELE, SELL, SPDYA, STAT1, TDP2, TGFBR2, TNFSF13B, TUBB3, VCP Cell Death and cytolysis 4.21E−04 ANXA1, CD244, CD46, CD47, FCER1A, GZMA, IFNAR1, MICA, NFE2L2, NR3C1, PPP3CB, PPP3R1, PTPRC, TGFBR2 14 Survival Cardiovascular regeneration of 4.91E−04 HMGB1, MTPN 2 System cardiomyocytes Development and Function, Cell Death and Survival, Cellular Development, Organ Morphology, Tissue Development, Tissue Morphology Cell Death and hemolysis 5.26E−04 ANXA1, CD47, IFNAR1, NFE2L2, NR3C1, PPP3CB, PPP3R1 7 Survival, Connective Tissue Disorders, Hematological Disease Cell Death and cell death of 5.41E−04 ANXA1, APAF1, ATM, CD47, CD74, CD86, CDC42, CFLAR, CYBB, CYLD, EIF2AK2, ERN1, FCER1A, GZMA, HMGB1, IFIH1, 33 Survival immune cells IFNAR1, IFNGR1, ITGA4, JAK2, KLF13, MCL1, MX1, NFE2L2, NR3C1, PARP14, PPP3CB, PTGER4, PTPRC, RAF1, STAT1, TGFBR2, TNFSF13B Cancer, Cell cell death of 8.29E−04 ANXA1, APAF1, ATM, CD47, CD74, CFLAR, EIF2AK2, HMGB1, JAK2, LRRK2, MCL1, NFE2L2, NR3C1, PARP14, PRNP, 18 Death and cancer cells RAF1, SELL, TNFSF13B Survival, Tumor Morphology Cell Death and cell death of 8.85E−04 APOBEC3B, CDC42, CFLAR, DAP3, EIF2AK2, ERN1, JAK2, MCL1, NFE2L2, PPP3R1, PRMT2, PRNP, RAD21, RAF1, 18 Survival kidney cell lines RNF13, RNF31, SLK, VCP Cell Death and cell viability of 9.22E−04 ATM, CDKL3, CDKN1C, CFLAR, CYBB, DUSP22, EPHB4, GLUD1, GPX1, HMGB1, IGFBP7, MCL1, MTMR1, MTMR6, 36 Survival tumor cell lines NFE2L2, NR3C1, PARP14, PPP1CC, PPP2CA, PPP2R5A, PPP4R1, PPP6C, PRNP, PSMA1, RAD21, RAF1, RBBP4, RICTOR, RIT1, RNF31, S100A6, TDP2, TGFBR2, TNFSF13B, TUBB3, VCP Cell Death and apoptosis of 9.87E−04 APAF1, ATM, ATP6V1G2, CFLAR, CYLD, DDX3X, EIF2AK2, EIF2S1, EPHX1, IFNAR1, MCL1, NFE2L2, NR3C1, PRNP, 19 Survival fibroblast cell PSMD6, RBL2, RNF13, STAT1, TAX1BP1 lines Cell Death and hemolytic 9.89E−04 ANXA1, CD47, IFNAR1, NR3C1, PPP3CB, PPP3R1 6 Survival, anemia Connective Tissue Disorders, Hematological Disease Cancer, Cell cell death of 1.00E−03 ANXA1, APAF1, ATM, CARD8, CD47, CD74, CFLAR, EIF2AK2, HMGB1, JAK2, LRRK2, MCL1, NFE2L2, NR3C1, PARP14, 21 Death and tumor cells PPP2CA, PRNP, RAF1, SELL, TGFBR2, TNFSF13B Survival, Tumor Morphology Cell Death and cell death of 1.27E−03 APAF1, ATM, ATP6V1G2, CDC42, CFLAR, CYLD, DDX3X, DDX58, EIF2AK2, EIF2S1, EPHX1, FNTA, GPX1, GZMA, 30 Survival connective IFNAR1, MCL1, NFE2L2, NR3C1, PRMT2, PRNP, PSMD6, RAF1, RBL2, RECQL, RNF13, SCP2, SLK, STAT1, TAX1BP1, VCP tissue cells Cell Death and degeneration of 1.45E−03 ARNTL, ATM 2 Survival, Cellular nerve ending Compromise, Neurological Disease, Tissue Morphology Cell Death and quantity of 1.45E−03 CD36, NFE2L2 2 Survival, apoptotic Respiratory pneumocytes Disease Cell Death and cell death of 1.50E−03 APAF1, ATM, ATP6V1G2, CFLAR, CYLD, DDX3X, EIF2AK2, EIF2S1, EPHX1, FNTA, IFNAR1, MCL1, NFE2L2, NR3C1, 23 Survival fibroblast cell PRNP, PSMD6, RBL2, RECQL, RNF13, SCP2, STAT1, TAX1BP1, VCP lines Cell Death and cell death of 1.50E−03 APAF1, ATM, CFLAR, CYLD, GZMA, KLF13, MCL1, NFE2L2, NR3C1, PTPRC 10 Survival thymocytes Cell Death and cell death of 1.52E−03 APAF1, APOBEC3B, ATM, CDC42, CFLAR, CTSS, CYLD, DAP3, EIF2AK2, ERN1, HMGB1, IFNGR1, JAK2, MC1R, MCL1, 25 Survival epithelial cells NFE2L2, NR3C1, PPP3R1, PRMT2, PRNP, RAD21, RAF1, RBL2, RNF31, TGFBR2 Cell Death and mitochondrial 1.57E−03 DDX58, MCL1, SRI 3 Survival cell death of tumor cell lines Cell Death and apoptosis of 1.61E−03 ANXA1, ATM, CD47, CDC42, CFLAR, CYBB, CYLD, EIF2AK2, FCER1A, GZMA, HMGB1, IFNGR1, JAK2, KLF13, MCL1, 23 Survival leukocytes NFE2L2, NR3C1, PPP3CB, PTGER4, PTPRC, RAF1, STAT1, TNFSF13B Cell Death and apoptosis of 1.73E−03 APAF1, ATM, BAZ1A, BRAT1, CARD8, CCAR1, CD47, CDC42, CDKN1C, CFLAR, CYLD, DDX58, EIF2AK2, EIF4G2, EPHB4, 52 Survival tumor cell lines ERN1, FCER1A, GLRX, GPX1, IGFBP7, JAK2, LMO4, MCL1, MTMR6, NFE2L2, NR3C1, OAS3, PARP14, PHIP, PPP2CA, PRNP, PTPRC, RAB32, RAD21, RAF1, RASSF3, RBL2, RICTOR, RIT1, RNF13, RNF31, RNF5, S100A6, SRI, STAT1, TDP2, TGFBR2, TMSB10/TMSB4X, TNFSF13B, TXNRD1, VCP, YWHAE Cell Death and autoimmune 1.78E−03 CD47, NR3C1, PPP3CB, PPP3R1 4 Survival, hemolytic Connective anemia Tissue Disorders, Hematological Disease, Immunological Disease Cell Death and cell viability of 1.89E−03 ATM, CDKL3, DUSP22, MCL1, MTMR1, MTMR6, PPP1CC, PPP2CA, PPP2R5A, PPP4R1, PPP6C, RAD21, TGFBR2 13 Survival cervical cancer cell lines Cell Death and cell death of 1.97E−03 APAF1, CCAR1, CDC42, CDKN1C, CFLAR, EPHB4, MCL1, RAF1, RASSF3, SRI, STAT1, TGFBR2, TMSB10/TMSB4X, 16 Survival colon cancer cell TXNRD1, VCP, YWHAE lines Cell Death and cell viability of 2.26E−03 CD47, CD74, CD86, CYLD, ERN1, FCER1A, HMGB1, JAK2, MCL1, MX1, PARP14, PTPRC, RAF1, STAT1, TNFSF13B 15 Survival leukocytes Cell Death and killing of natural 2.42E−03 CD244, IFNAR1, IFNGR1, STAT1 4 Survival killer cells Cell Death and cell death of 2.46E−03 ANXA1, CFLAR, CYBB, EIF2AK2, FCER1A, HMGB1, IFNAR1, JAK2, MCL1, NFE2L2, NR3C1, RAF1, STAT1 13 Survival myeloid cells Cell Death and cell death of 2.68E−03 APOBEC3B, CDC42, CFLAR, DAP3, EIF2AK2, ERN1, JAK2, MCL1, NFE2L2, PPP3R1, PRMT2, PRNP, RAD21, RAF1, 16 Survival epithelial cell RNF31, TGFBR2 lines Cell Death and necrosis of 2.81E−03 APAF1, APOBEC3B, ATM, CD36, CDC42, CFLAR, CTSS, CYLD, DAP3, EIF2AK2, ERN1, GPX1, HMGB1, IFNGR1, JAK2, 28 Survival epithelial tissue MC1R, MCL1, NFE2L2, NR3C1, PPP3R1, PRMT2, PRNP, PSMB8, RAD21, RAF1, RBL2, RNF31, TGFBR2 Cell Death and cell viability of 2.85E−03 CD47, CD74, CD86, CYLD, ERN1, FCER1A, HMGB1, JAK2, MCL1, MX1, PARP14, PTPRC, RAF1, SELE, STAT1, TNFSF13B 16 Survival blood cells Cell Death and cytotoxicity 2.87E−03 CALM1 (includes others), CD244, CD46, CD74, CFLAR, CYBB, FKBP1A, GZMA, 14 Survival HLA-DRB1, IFNAR1, MICA, PTPRC, STAT1, TGFBR2 Cell Death and cell death of 2.97E−03 APOBEC3B, CDC42, CFLAR, DAP3, EIF2AK2, ERN1, IFNAR1, MCL1, NFE2L2, PPP3R1, PRMT2, PRNP, RAD21, RNF31 14 Survival, embryonic cell Embryonic lines Development Cancer, Cell cell death of 3.42E−03 ATM, CD47, JAK2, MCL1, RAF1, SELL, TNFSF13B 7 Death and leukemia cells Survival, Tumor Morphology Cell Death and cytotoxicity of 3.51E−03 CALM1 (includes others), CD244, CD46, CD74, CFLAR, CYBB, GZMA, HLA-DRB1, 13 Survival, Cellular cells IFNAR1, MICA, PTPRC, STAT1, TGFBR2 Compromise Cell Death and killing of 3.74E−03 CD244, CD47, IFNAR1, IFNGR1, STAT1 5 Survival lymphocytes Cell Death and apoptosis of 3.99E−03 APAF1, ATM, CDC42, CFLAR, DDX58, EIF2AK2, EIF2S1, GZMA, MCL1, PRMT2, RAF1, SLK 12 Survival fibroblasts Cell Death and cell death of 4.36E−03 APAF1, ATM, CDC42, CFLAR, DDX58, EIF2AK2, EIF2S1, EPHX1, GPX1, GZMA, MCL1, PRMT2, RAF1, SLK 14 Survival fibroblasts Cell Death and activation of 4.56E−03 APAF1, CARD8, JAK2, MTCH1, STAT1, VCP 6 Survival, Cell caspase Signaling Cancer, Cell cell viability of 4.64E−03 CD74, HMGB1, MCL1, NFE2L2, PARP14, SELL, TNFSF13B 7 Death and cancer cells Survival, Tumor Morphology Cancer, Cell cell death of 4.68E−03 ATM, CD47, SELL, TNFSF13B 4 Death and chronic Survival, Tumor lymphocytic Morphology leukemia cells Cell Death and cytolysis of 4.70E−03 CD244, MICA 2 Survival lymphoblastoid cell lines Cell Death and loss of B 4.70E−03 CD74, SPPL2A 2 Survival lymphocytes Cell Death and cell death of T 5.03E−03 APAF1, ATM, CD47, CDC42, CFLAR, CYLD, GZMA, IFNGR1, KLF13, MCL1, NFE2L2, NR3C1, PPP3CB, PTPRC, 16 Survival lymphocytes STAT1, TGFBR2 Cancer, Cell cell viability of 5.07E−03 CD74, HMGB1, LRRK2, MCL1, NFE2L2, PARP14, SELL, TNFSF13B 8 Death and tumor cells Survival, Tumor Morphology Cell Death and cell death of 5.35E−03 APAF1, ATM, CD47, CDC42, CFLAR, CYLD, EIF2AK2, FCER1A, GZMA, IFNGR1, KLF13, MCL1, NFE2L2, NR3C1, 19 Survival mononuclear PPP3CB, PTPRC, STAT1, TGFBR2, TNFSF13B leukocytes Cell Death and apoptosis of 5.39E−03 APAF1, CCAR1, CDC42, CDKN1C, CFLAR, EPHB4, MCL1, RASSF3, SRI, STAT1, TMSB10/TMSB4X, VCP, YWHAE 13 Survival colon cancer cell lines Cell Death and cell death of 5.46E−03 ANXA1, CFLAR, CYBB, EIF2AK2, FCER1A, HMGB1, IFNAR1, MCL1, NFE2L2, NR3C1, PTGER4, STAT1 12 Survival phagocytes Cell Death and apoptosis of 5.60E−03 ANXA1, CFLAR, CYBB, EIF2AK2, FCER1A, HMGB1, JAK2, MCL1, NFE2L2, RAF1, STAT1 11 Survival myeloid cells Cell Death and apoptosis of 6.47E−03 ATM, CFLAR, CYLD, GZMA, KLF13, NFE2L2, NR3C1, PTPRC 8 Survival thymocytes Cell Death and apoptosis of 6.50E−03 CFLAR, DAP3, EIF2AK2, JAK2, MCL1, NFE2L2, PPP3R1, PRMT2, RAD21, RAF1, RNF13, RNF31, SLK 13 Survival kidney cell lines Cell Death and necroptosis of 6.94E−03 CYLD, STAT1 2 Survival tumor cell lines Cell Death and fragmentation 7.93E−03 APOBEC3B, EIF2AK2, GZMA, MTCH1, PPP1CC 5 Survival, DNA of DNA Replication, fragment Recombination, and Repair Cell Death and apoptosis of 8.07E−03 CFLAR, MCL1, NFE2L2 3 Survival peritoneal macrophages Cancer, Cell apoptosis of 8.20E−03 ATM, JAK2, MCL1, RAF1, SELL, TNFSF13B 6 Death and leukemia cells Survival, Tumor Morphology Cell Death and cell death of 8.22E−03 APAF1, ATM, CD47, CDC42, CFLAR, CYLD, EIF2AK2, GZMA, IFNGR1, KLF13, MCL1, NFE2L2, NR3C1, PPP3CB, PTPRC, 18 Survival lymphocytes STAT1, TGFBR2, TNFSF13B Cancer, Cell cell viability of 9.34E−03 CD74, SELL, TNFSF13B 3 Death and chronic Survival, Tumor lymphocytic Morphology leukemia cells Cell Death and cell death of 9.40E−03 APAF1, ATM, CFLAR, CYLD, EIF2AK2, GZMA, KLF13, MCL1, NFE2L2, NR3C1, PTPRC, RAF1 12 Survival hematopoietic cells Cell Death and neurodegen- 9.58E−03 ATM, PRNP 2 Survival, Cellular eration of Compromise, granule cells Neurological Disease, Organismal Injury and Abnormalities, Tissue Morphology Cell Death and apoptosis of 9.98E−03 CFLAR, DAP3, EIF2AK2, JAK2, MCL1, NFE2L2, PPP3R1, PRMT2, RAD21, RAF1, RNF31, TGFBR2 12 Survival epithelial cell lines Cell Death and apoptosis of 1.05E−02 CARD8, CFLAR, EIF2AK2, ERN1, FCER1A, IGFBP7, JAK2, MCL1, PTPRC, TNFSF13B 10 Survival lymphoma cell lines Cell-To-Cell activation of 6.10E−08 ANXA1, ATM, BLOC1S6, CD244, CD36, CD46, CD47, CD58, CD74, CD86, CLEC7A, CTSS, CYBB, DDX58, ERAP1, FKBP1A, 45 Signaling and leukocytes GZMA, HBP1, HLA-DMA, HLA-DMB, HLA-DQA1, HLA-DRB1, Interaction, HMGB1, IFNAR1, JAK2, MGST1, MICA, NBR1, NDFIP1, NFE2L2, PELI1, PPP3CB, PRNP, PSMB8, PTGER4, PTPRC, Hematological RAB10, RAB32, RAB6A, RAB8B, SELE, SELL, STAT1, TGFBR2, TNFSF13B System Development and Function, Immune Cell Trafficking, Inflammatory Response Cell-To-Cell activation of 1.61E−07 ANXA1, ATM, BLOC1S6, CD244, CD36, CD46, CD47, CD58, CD74, CD86, CLEC7A, CTSS, CYBB, DDX58, ERAP1, FKBP1A, 46 Signaling and blood cells GZMA, HBP1, HLA-DMA, HLA-DMB, HLA-DQA1, HLA-DRB1, Interaction, HMGB1, IFNAR1, JAK2, MGST1, MICA, NBR1, NDFIP1, NFE2L2, PELI1, PLEK, PPP3CB, PRNP, PSMB8, PTGER4, Hematological PTPRC, RAB10, RAB32, RAB6A, RAB8B, SELE, SELL, STAT1, TGFBR2, TNFSF13B System Development and Function Cell-To-Cell activation of 4.70E−07 ANXA1, ATM, BLOC1S6, CD244, CD36, CD46, CD47, CD58, CD74, CD86, CLEC7A, CTSS, CYBB, CYLD, DDX58, EIF2AK2, 55 Signaling and cells ERAP1, ERN1, FCER1A, FKBP1A, FNTA, GPX1, GZMA, HBP1, HLA-DMA, HLA-DMB, HLA-DQA1, HLA-DRB1, Interaction HMGB1, IFNAR1, JAK2, MGST1, MICA, MTCH1, NBR1, NDFIP1, NFE2L2, PELI1, PLEK, PPP2CA, PPP3CB, PRNP, PSMB8, PTGER4, PTPRC, RAB10, RAB32, RAB6A, RAB8B, RICTOR, SELE, SELL, STAT1, TGFBR2, TNFSF13B Cell-To-Cell activation of 5.45E−07 ATM, CD36, CD47, CD74, CD86, CLEC7A, CTSS, CYBB, ERAP1, HBP1, HLA-DMA, HLA-DMB, HLA-DQA1, 25 Signaling and antigen HMGB1, IFNAR1, JAK2, PELI1, PRNP, PSMB8, PTGER4, RAB10, RAB32, RAB6A, RAB8B, STAT1 Interaction, presenting cells Hematological System Development and Function, Immune Cell Trafficking, Inflammatory Response Antimicrobial antiviral 1.08E−05 DDX58, IFNAR1, STAT1 3 Response, Cell- response of To-Cell Signaling fibroblasts and Interaction, Connective Tissue Development and Function, Inflammatory Response Cell-To-Cell recruitment of 2.61E−05 ANXA1, CD36, CD47, CD74, CLEC7A, DDX58, FCER1A, GLRX, HDC, HMGB1, IFNAR1, ITGA4, 21 Signaling and leukocytes LRRK2, NFE2L2, PELI1, PRMT2, RAP1A, ROCK1, SELE, SELL, TGFBR2 Interaction, Cellular Movement, Hematological System Development and Function, Immune Cell Trafficking Cell-To-Cell adhesion of 6.76E−05 ANXA1, ANXA7, CD36, CD46, CD47, CD58, CD74, CDC42, CYBB, GALNT1, GLRX, HMGB1, IFNGR1, ITGA4, JAK2, 24 Signaling and blood cells PAFAH1B1, PTGER4, PTPRC, RICTOR, ROCK1, SELE, SELL, STAT1, TGFBR2 Interaction, Tissue Development Cell-To-Cell adhesion of 1.31E−04 ANXA1, CD36, CD46, CD47, CD58, CD74, CDC42, GALNT1, GLRX, HMGB1, IFNGR1, ITGA4, JAK2, PAFAH1B1, PTGER4, 22 Signaling and immune cells PTPRC, RICTOR, ROCK1, SELE, SELL, STAT1, TGFBR2 Interaction, Hematological System Development and Function, Immune Cell Trafficking, Tissue Development Cell-To-Cell activation of 1.39E−04 ANXA1, BLOC1S6, CD244, CD46, CD47, CD58, CD74, CD86, CLEC7A, DDX58, GZMA, HLA-DRB1, 26 Signaling and lymphocytes HMGB1, IFNAR1, MGST1, MICA, NBR1, NDFIP1, NFE2L2, PELI1, PPP3CB, PRNP, PTPRC, STAT1, TGFBR2, TNFSF13B Interaction, Hematological System Development and Function, Immune Cell Trafficking, Inflammatory Response Cell-To-Cell adhesion of 2.18E−04 ANXA1, CD47, CD58, HMGB1, IFNGR1, ITGA4, JAK2, RICTOR, ROCK1, SELE, SELL, TGFBR2 12 Signaling and mononuclear Interaction, leukocytes Hematological System Development and Function, Immune Cell Trafficking, Tissue Development Cell-To-Cell activation of T 2.25E−04 ANXA1, CD244, CD46, CD47, CD58, CD74, CD86, CLEC7A, DDX58, GZMA, HLA-DRB1, 21 Signaling and lymphocytes IFNAR1, MGST1, NBR1, NDFIP1, NFE2L2, PPP3CB, PRNP, PTPRC, STAT1, TGFBR2 Interaction, Hematological System Development and Function, Immune Cell Trafficking, Inflammatory Response Cell-To-Cell adhesion of T 3.06E−04 ANXA1, CD47, CD58, IFNGR1, ITGA4, JAK2, RICTOR, SELE, SELL 9 Signaling and lymphocytes Interaction, Cell- mediated Immune Response, Cellular Movement, Hematological System Development and Function, Immune Cell Trafficking, Tissue Development Cell-To-Cell response of 3.84E−04 ABCA7, ANXA1, CD36, CD47, CLEC7A, DDX58, ERN1, FCER1A, GLRX, HMGB1, IFNAR1, ITGA4, NR3C1, ZEB2 14 Signaling and phagocytes Interaction, Inflammatory Response Cell-To-Cell adhesion of 4.20E−04 ANXA1, CD47, CD58, IFNGR1, ITGA4, JAK2, RICTOR, ROCK1, SELE, SELL 10 Signaling and lymphocytes Interaction, Hematological System Development and Function, Immune Cell Trafficking, Tissue Development Cell-To-Cell phagocytosis of 4.51E−04 ANXA1, CD36, CD47, GLRX, HMGB1, IFNAR1 6 Signaling and granulocytes Interaction, Cellular Function and Maintenance, Hematological System Development and Function, Inflammatory Response Cell-To-Cell response of 4.52E−04 CD36, DDX58, IFNAR1, STAT1 4 Signaling and fibroblasts Interaction, Connective Tissue Development and Function Cell-To-Cell phagocytosis of 4.91E−04 CD47, HMGB1 2 Signaling and bone marrow- Interaction, derived Cellular Function neutrophils and Maintenance, Hematological System Development and Function, Inflammatory Response Cardiovascular adhesion of 5.03E−04 ANXA7, CD36, CDC42, HMGB1, IGFBP7, ITGA4, RICTOR, SELE, SELL, TGFBR2, TMSB10/TMSB4X 11 System endothelial cells Development and Function, Cell-To- Cell Signaling and Interaction, Tissue Development Cell-To-Cell response of 5.49E−04 ABCA7, ANXA1, CD36, CD47, DDX58, ERN1, FCER1A, GLRX, HMGB1, IFNAR1, ITGA4, NR3C1, PTPRC 13 Signaling and myeloid cells Interaction Cell-To-Cell detachment of 8.24E−04 ANXA1, PTPRC, SELL 3 Signaling and leukocytes Interaction, Hematological System Development and Function, Immune Cell Trafficking, Tissue Development Cell-To-Cell immune 8.55E−04 ABCA7, ANXA1, CD36, CD47, CD86, CTSS, DDX58, ERN1, FCER1A, GLRX, HMGB1, IFNAR1, IFNGR1, ITGA4, NR3C1, 17 Signaling and response of PTPRC, TGFBR2 Interaction, leukocytes Inflammatory Response Cardiovascular adhesion of 9.38E−04 ANXA7, CD36, HMGB1, IGFBP7, ITGA4, RICTOR, SELE, TMSB10/TMSB4X 8 System vascular Development and endothelial cells Function, Cell-To- Cell Signaling and Interaction, Tissue Development Cell-To-Cell immune 1.30E−03 ABCA7, ANXA1, CD36, CD47, DDX58, ERN1, FCER1A, GLRX, HMGB1, IFNAR1, ITGA4, NR3C1 12 Signaling and response of Interaction, phagocytes Inflammatory Response Cell-To-Cell response of 1.33E−03 ANXA1, CD36, CD47, FCER1A, GLRX, HMGB1, IFNAR1, ITGA4 8 Signaling and granulocytes Interaction Cell-To-Cell immune 1.37E−03 CD36, CD47, FCER1A, GLRX, HMGB1, IFNAR1, ITGA4 7 Signaling and response of Interaction, neutrophils Hematological System Development and Function, Inflammatory Response Cell-To-Cell response of 1.42E−03 ABCA7, ANXA1, CD36, CD47, CLEC7A, CTSS, DDX58, ERN1, HMGB1, IFNAR1, NR3C1 11 Signaling and antigen Interaction presenting cells Cell-To-Cell recruitment of 1.80E−03 CD47, DDX58, FCER1A, HDC, HMGB1, ITGA4, PELI1, SELE, SELL 9 Signaling and mononuclear Interaction, leukocytes Cellular Movement, Hematological System Development and Function, Immune Cell Trafficking Cell-To-Cell immune 2.03E−03 ABCA7, ANXA1, CD36, CD47, CTSS, DDX58, ERN1, HMGB1, IFNAR1, NR3C1 10 Signaling and response of Interaction, antigen Inflammatory presenting cells Response Cell-To-Cell binding of B- 2.05E−03 CD47, CRKL, ITGA4 3 Signaling and lymphocyte Interaction, derived cell lines Hematological System Development and Function Cell Cycle, Cell- contact growth 2.05E−03 HMGB1, IKZF1, PTPRC 3 To-Cell Signaling inhibition of and Interaction, leukocytes Cellular Growth and Proliferation Cell-To-Cell phagocytosis of 2.53E−03 CD36, CD47, GLRX, HMGB1, IFNAR1 5 Signaling and neutrophils Interaction, Cellular Function and Maintenance, Hematological System Development and Function, Inflammatory Response Cell-To-Cell cell-cell 2.80E−03 ITGA4, PTPRC, ROCK1, SELE 4 Signaling and adhesion of Interaction, leukocytes Hematological System Development and Function, Immune Cell Trafficking, Tissue Development Cardiovascular adhesion of 2.86E−03 SELE, SELL 2 System HCAEC cells Development and Function, Cell-To- Cell Signaling and Interaction, Tissue Development Cell-To-Cell adhesion of 2.86E−03 SELE, SELL 2 Signaling and acute myeloid Interaction, leukemia blast Cellular cells Compromise, Tissue Development, Tumor Morphology Cell-To-Cell afterhyperpolari- 2.86E−03 ATP2B4, LMO4 2 Signaling and zation of central Interaction, nervous system Nervous System cells Development and Function Cell-To-Cell detachment of 2.86E−03 ANXA1, PTPRC 2 Signaling and phagocytes Interaction, Cellular Movement, Hematological System Development and Function, Immune Cell Trafficking, Tissue Development Cell-To-Cell recruitment of 2.86E−03 DDX58, PELI1 2 Signaling and CD8+ T Interaction, Cell- lymphocyte mediated Immune Response, Cellular Movement, Hematological System Development and Function, Immune Cell Trafficking Cell Cycle, Cell- contact growth 3.09E−03 CDC42, GBP2, HMGB1, IKZF1, ING4, JAK2, PTPRC, RAF1, RBL2, STAT1 10 To-Cell Signaling inhibition and Interaction, Cellular Growth and Proliferation Cell-To-Cell fusion of 3.21E−03 CD36, CD46, CD47, STAT1 4 Signaling and leukocytes Interaction, Hematological System Development and Function, Immune Cell Trafficking, Infectious Disease, Tissue Development Cell-To-Cell response of 3.89E−03 ABCA7, ANXA1, CD36, CD47, CLEC7A, DDX58, ERN1, HMGB1, NR3C1 9 Signaling and macrophages Interaction, Inflammatory Response Cell-To-Cell phagocytosis of 4.10E−03 ABCA7, ANXA1, CD302, CD36, CD47, CDC42, CLEC7A, CLTC, DNTTIP1, GLRX, HMGB1, IFNAR1, LY75, NR3C1 14 Signaling and cells Interaction, Cellular Function and Maintenance, Inflammatory Response Cell-To-Cell binding of blood 4.16E−03 CD47, CD58, CD86, HLA-DMA, HMGB1, IFNGR1, ITGA4, JAK2, NFE2L2, PTPRC, RAP1B, SELE, SELL 13 Signaling and cells Interaction Cell-To-Cell binding of T 4.25E−03 CD47, CD58, CD86, HLA-DMA, IFNGR1, ITGA4 6 Signaling and lymphocytes Interaction, Hematological System Development and Function, Tissue Development Cell-To-Cell adhesion of 4.49E−03 HMGB1, ROCK1, SELE, SELL, TGFBR2 5 Signaling and monocytes Interaction, Hematological System Development and Function, Immune Cell Trafficking, Inflammatory Response, Tissue Development Cell-To-Cell recruitment of T 4.56E−03 CD47, DDX58, FCER1A, HDC, PELI1, SELE 6 Signaling and lymphocytes Interaction, Cell- mediated Immune Response, Cellular Movement, Hematological System Development and Function, Immune Cell Trafficking Cell-To-Cell afterhyperpolari- 4.70E−03 ATP2B4, LMO4 2 Signaling and zation of Interaction, neurons Nervous System Development and Function Cell Cycle, Cell- contact growth 4.70E−03 RAF1, STAT1 2 To-Cell Signaling inhibition of and Interaction, melanoma cell Cellular Growth lines and Proliferation Cell-To-Cell suppression of 4.70E−03 CD46, CD86 2 Signaling and effector T Interaction, lymphocytes Cellular Growth and Proliferation, Hematological System Development and Function Cell-To-Cell binding of 5.07E−03 CD47, CD58, CD86, HLA-DMA, IFNGR1, ITGA4, SELE, SELL 8 Signaling and mononuclear Interaction, leukocytes Hematological System Development and Function Cell-To-Cell binding of 5.22E−03 CD47, CD58, CD86, HLA-DMA, IFNGR1, ITGA4, SELL 7 Signaling and lymphocytes Interaction, Hematological System Development and Function Cell-To-Cell recruitment of 5.52E−03 CD47, DDX58, FCER1A, HDC, PELI1, SELE, SELL 7 Signaling and lymphocytes Interaction, Cellular Movement, Hematological System Development and Function, Immune Cell Trafficking Cell-To-Cell adhesion of 5.85E−03 ANXA1, GLRX, HMGB1, ITGA4, PAFAH1B1, ROCK1, SELE, SELL, TGFBR2 9 Signaling and phagocytes Interaction, Hematological System Development and Function, Immune Cell Trafficking, Inflammatory Response, Tissue Development Cell-To-Cell binding of 5.85E−03 CD47, ITGA4, RAP1B 3 Signaling and hematopoietic Interaction, progenitor cells Hematological System Development and Function, Hematopoiesis Cell-To-Cell binding of 6.81E−03 CD36, CD47, ITGA4, JAK2, SELL 5 Signaling and leukemia cell Interaction lines Cell-To-Cell binding of bone 6.90E−03 CRKL, ITGA4, RAF1 3 Signaling and marrow cell Interaction lines Cell-To-Cell adhesion of Th1 6.94E−03 ITGA4, SELE 2 Signaling and cells Interaction, Cell- mediated Immune Response, Cellular Movement, Hematological System Development and Function, Immune Cell Trafficking, Tissue Development Antigen antigen 6.94E−03 CTSS, IFNAR1 2 Presentation, presentation of Cell-To-Cell antigen Signaling and presenting cells Interaction, Inflammatory Response Cell-To-Cell detachment of 6.94E−03 ANXA1, PTPRC 2 Signaling and myeloid cells Interaction, Hematological System Development and Function, Immune Cell Trafficking, Tissue Development Cell-To-Cell response of 6.94E−03 FCER1A, ZEB2 2 Signaling and mast cells Interaction, Inflammatory Response Cell-To-Cell immune 7.11E−03 ABCA7, ANXA1, CD36, CD47, DDX58, ERN1, HMGB1, NR3C1 8 Signaling and response of Interaction, macrophages Inflammatory Response Cell-To-Cell recognition of 7.26E−03 CD36, CD47, CLEC7A, MICA 4 Signaling and cells Interaction Cell-To-Cell activation of 7.34E−03 ANXA1, ATM, CD36, CD47, CD86, CLEC7A, CYBB, FKBP1A, GZMA, HMGB1, IFNAR1, JAK2, PELI1, PRNP, PTGER4, SELE, 18 Signaling and phagocytes SELL, STAT1 Interaction, Hematological System Development and Function, Immune Cell Trafficking, Inflammatory Response Cell-To-Cell binding of B 8.07E−03 CD47, CD86, ITGA4 3 Signaling and lymphocytes Interaction, Hematological System Development and Function, Humoral Immune Response Cardiovascular adhesion of 9.58E−03 CD74, SELL 2 System postcapillary Development and venule Function, Cell-To- Cell Signaling and Interaction, Tissue Development Cell Cycle, Cell- contact growth 9.58E−03 IKZF1, PTPRC 2 To-Cell Signaling inhibition of and Interaction, lymphocytes Cellular Growth and Proliferation Cell-To-Cell phagocytosis of 1.06E−02 ABCA7, ANXA1, CD36, CD47, CDC42, GLRX, HMGB1, IFNAR1 8 Signaling and blood cells Interaction, Cellular Function and Maintenance, Inflammatory Response Cell-To-Cell phagocytosis of 1.14E−02 ABCA7, ANXA1, CD36, CD47, GLRX, HMGB1, IFNAR1 7 Signaling and phagocytes Interaction, Cellular Function and Maintenance, Inflammatory Response Cell-To-Cell fusion of cells 1.15E−02 ANXA1, CD36, CD46, CD47, IFRD1, ROCK1, STAT1, UBE2B 8 Signaling and Interaction

TABLE 1 Differentiated Exon Usage in the 5 Groups (p < 0.005, |FC| > 1.2) Marker ID Gene Symbol Entrez GeneID Ensembl UniProtKB Table 1A: Exon Usage Upregulated in Cardioembolic Ischemic Stroke (CE IS) chr17.73000302-73002233>CDR2L CDR2L 30850 ENSG00000109089 Q86X02 chr8.104406853-104407319>shuskeebu shuskeebu “NoInfo” “NoInfo” “NoInfo” chr3.48456585-48456756>PLXNB1 PLXNB1 5364 ENSG00000164050 O43157 chr1.86861716-86861978>ODF2L ODF2L 57489 ENSG00000122417 Q9ULJ1 chr19.58427747- 147687 and 58427959>ZNF417andZNF814 ZNF417 and ZNF814 730051 ENSG00000173480 and Q8TAU3 and B7Z6K7 ENSG00000204514 chr19.58427747- 147687 and 730051 ENSG00000173480 and Q8TAU3 and B7Z6K7 58427960>ZNF417andZNF814 ZNF417 and ZNF814 ENSG00000204514 chr22.19115606-19115962>skatee skatee “NoInfo” “NoInfo” “NoInfo” chr10.49253461-49254183>BMS1P7 BMS1P7 100133265 ENSG00000243899 chr14.70242552-70243105>SLC10A1 SLC10A1 6554 ENSG00000100652 Q14973 chr7.142630429-142630905>TRPV5 TRPV5 56302 ENSG00000127412 Q9NQA5 chr10.38299602-38299711>ZNF33A ZNF33A 7581 ENSG00000189180 Q06730 chr10.38299604-38299711>ZNF33A ZNF33A 7581 ENSG00000189180 Q06730 chr2.119988299-119988610>STEAP3 STEAP3 55240 ENSG00000115107 Q658P3 chr2.179463448-179463831>CCDC141andTTN CCDC141 and TTN 285025 and 7273 ENSG00000163492 and Q6ZP82 and Q8WZ42 ENSG00000155657 chr2.25258142-25260098>LOC729723 LOC729723 “NoInfo” “NoInfo” “NoInfo” chr17.34856670-34856799>MYO19 MYO19 80179 ENSG00000141140 Q96H55 chr7.158334118-158334468>PTPRN2 PTPRN2 5799 ENSG00000155093 Q92932 chr3.188326949-188327339>LPP LPP 4026 ENSG00000145012 Q93052 chr19.18959976-18960255>UPF1 UPF1 5976 ENSG00000005007 Q92900 chr6.37225553-37225749>TBC1D2213 TBC1D226 55633 ENSG00000065491 Q9NU19 chr20.43995515-43996064>SYS1-DBNDD2 SYS1-DBNDD2 767557 ENSG00000254806 H3BUS1 chr3.49448633-49449166>myforbo myforbo “NoInfo” “NoInfo” “NoInfo” chr4.15570247-15570813>klawgu klawgu “NoInfo” “NoInfo” “NoInfo” Table 1B: Exon Usage Upregulated in Large Vessel Ischemic Stroke (LV IS) chr6.37225553-37225749>TBC1D22B TBC1D22B 55633 ENSG00000065491 Q9NU19 chr20.43995515-43996064>SYS1-DBNDD2 SYS1-DBNDD2 767557 ENSG00000254806 H3BUS1 chr3.49448633-49449166>myforbo myforbo “NoInfo” “NoInfo” “NoInfo” chr4.15570247-15570813>klawgu klawgu “NoInfo” “NoInfo” “NoInfo” chr14.53248502-53248629>GNPNAT1 GNPNAT1 64841 ENSG00000100522 Q96EK6 chr22.29141852-29141989>HSCB HSCB 150274 ENSG00000100209 Q8IWL3 chr16.72146312-72146549>DHX38 DHX38 9785 ENSG00000140829 Q92620 chr5.176715528-176715926>NSD1 NSD1 64324 ENSG00000165671 Q96L73 chr6.100023529-100023947>RPS3P5 RPS3P5 100131956 ENSG00000219755 “NoInfo” chr13.103506107-103506222>BIVMandERCC5 BIVM and ERCC5 54841 and 2073 ENSG00000134897 and Q86UB2 and P28715 ENSG00000134899 chr7.2282560-2282683>NUDT1 NUDT1 4521 ENSG00000106268 P36639 chr12.54645834-54646011>CBX5 CBX5 23468 ENSG00000094916 P45973 chr20.33056659-33057236>vytaw vytaw “NoInfo” “NoInfo” “NoInfo” chr5.162902464-162902678>HMMR HMMR 3161 ENSG00000072571 O75330 chr11.62389338-62389648>B3GAT3 B3GAT3 26229 ENSG00000149541 O94766 chr15.101847418-101849508>PCSK6 PCSK6 5046 ENSG00000140479 P29122 chr5.61688639-61688817>DIMT1L DIMT1L (DIMT1) 27292 ENSG00000086189 Q9UNQ2 chr12.56334947-56335109>DGKA DGKA 1606 ENSG00000065357 P23743 chr10.46918169- FAM35B(FAM35BP) 414241 and 6008 ENSG00000165874 and 46918362>FAM35BandRHEBP1 and RHEBP1 ENSG00000229927 chr2.20756227-20757428>dawgorbu dawgorbu “NoInfo” “NoInfo” “NoInfo” chrX.152226503-152227128>PNMA3 PNMA3 29944 ENSG00000183837 Q9UL41 chr22.18613610-18614498>PEX26andTUBA8 PEX26 and TUBA8 55670 and 51807 ENSG00000183785 ENSG00000215193 and Q7Z412 and Q9NY65 chr6.111619174-111619773>slyjey slyjey “NoInfo” “NoInfo” “NoInfo” chr17.43002077-43003867>KIF18B KIF18B 146909 ENSG00000186185 Q86Y91 chr8.90798887-90799401>RIPK2 RIPK2 8767 ENSG00000104312 O43353 chr1.214836934-214837426>CENPF CENPF 1063 ENSG00000117724 P49454 chr3.8606070-8609805>LMCD1 LMCD1 29995 ENSG00000071282 Q9NZU5 chr20.52560545-52561535>BCAS1 BCAS1 8537 ENSG00000064787 O75363 chr2.173420100-173420447>PDK1 PDK1 5163 ENSG00000152256 Q15118 chr15.81584265-81585378>IL16 IL16 3603 ENSG00000172349 Q14005 chr9.131486273-131486409>ZDHHC12 ZDHHC12 84885 ENSG00000160446 Q96GR4 chr16.4475881-4476093>DNAJA3 DNAJA3 9093 ENSG00000103423 Q96EY1 Table 1C: Exon Usage Upregulated in Lacunar Ischemic Stroke (L IS) chr11.119039480-119040011>NLRX1 NLRX1 79671 ENSG00000160703 Q86UT6 chr15.52970203-52970319>KIAA1370 KIAA1370 56204 ENSG00000047346 Q32MH5 (FAM214A) chr11.62475067-62475387>GNG3 GNG3 2785 ENSG00000162188 P63215 chr12.94914730-94915694>LOC400061 LOC400061 400061 ENSG00000258357 “NoInfo” chr16.15013757-15013940>zoner zoner “NoInfo” “NoInfo” “NoInfo” chr2.29258330-29258510>FAM179A FAM179A 165186 ENSG00000189350 Q6ZUX3 chr18.33077683-33077895>INO80C INO80C 125476 ENSG00000153391 Q6P198 chr2.160143094-160143317>WDSUB1 WDSUB1 151525 ENSG00000196151 Q8N9V3 chr22.44514918-44515020>PARVB PARVB 29780 ENSG00000188677 Q9H611 chr5.156821041-156822687>ADAM19 ADAM19 8728 ENSG00000135074 Q9H013 chr6.146285293-146285559>SHPRH SHPRH 257218 ENSG00000146414 Q149N8 chr6.146285293-146285525>SHPRH SHPRH 257218 ENSG00000146414 Q149N8 chr22.24316496-24316679>GSTTP1andDDT GSTTP1 and DDT 25774 and 1652 ENSG00000241850 and “NoInfo” and P30046 ENSG00000099977 chr12.2966630-2968829>FOXM1 FOXM1 2305 ENSG00000111206 Q08050 chr7.99674926-99675056>ZNF3 ZNF3 7551 ENSG00000166526 P17036 chr6.30610545-30612432>C6orf134 C6orf134 (ATAT1) 79969 ENSG00000137343 Q5SQ10 chr19.35173682-35173954>ZNF302 ZNF302 55900 ENSG00000089335 Q9NR11 chr21.47706315-47706712>C210rf57 C21orf57 (YBEY) 54059 ENSG00000182362 P58557 chr12.111065735-111066029>TCTN1 TCTN1 79600 ENSG00000204852 Q2MV58 chrX.40495835-40495964>CXorf38 CXorf38 159013 ENSG00000185753 Q8TB03 chr9.46687439-46688197>KGFLP1 KGFLP1 387628 ENSG00000227449 Q2TVT4 chr2.101627502-101628002>TBC1D8 TBC1D8 11138 ENSG00000204634 095759 chr1.160580214-160580588>SLAMF1 SLAMF1 6504 ENSG00000117090 Q13291 chr8.10340434-10340741>LOC346702 LOC346702 “NoInfo” “NoInfo” “NoInfo” chr6.168370462-168372588>MLLT4 MLLT4 4301 ENSG00000130396 P55196 chr1.155691308-155691471>DAP3 DAP3 7818 ENSG00000132676 P5139 chr12.123262038-123262230>CCDC62 CCDC62 84660 ENSG00000130783 Q6P9F0 chr14.96795821-96795971>ATG2B ATG2B 55102 ENSG00000066739 Q96BY7 chr20.32079185-32079982>spawvor spawvor “NoInfo” “NoInfo” “NoInfo” chr6.163984476-163984751>QKI QKI 9444 ENSG00000112531 Q96PU8 chr1.246729640-246730091>CNST CNST 163882 ENSG00000162852 Q6PJW8 Table 1D: Exon Usage Upregulated in Intracerebral Hemorrhage (ICH) chr19.44128266-44128394>CADM4 CADM4 199731 ENSG00000105767 Q8NFZ8 chr5.139929370-139930496>APBB3andSRA1 APBB3 and SRA1 10307 and 10011 ENSG00000213523 ENSG00000113108 and O95704 and Q9HD15 chr1.85127881-85128058>SSX2IP SSX2IP 117178 ENSG00000117155 Q9Y2D8 chr22.31733654-31734031>sneypoy sneypoy “NoInfo” “NoInfo” “NoInfo” chr17.40280569-40280818>RAB5C RAB5C 5878 ENSG00000108774 P51148 chr3.23929058-23929280>UBE2E1 UBE2E1 7324 ENSG00000170142 P51965 chr7.149598-152547>kehera kehera “NoInfo” “NoInfo” “NoInfo” chr3.122283274-122283460>DTX3L DTX3L 151636 ENSG00000163840 Q8TDB6 chr14.76107075- FLVCR2 and TILLS 55640 and 23093 ENSG00000119685 and ENSG00000119686 and 76107403>FLVCR2andTTLL5andC14orf179 and C14orf179 (IFT43) and 112752 ENSG00000119650 Q9UPI3 and Q6EMB2 and Q96FT9 chr1.235956803-235956912>LYST LYST 1130 ENSG00000143669 Q99698 chr2.198175302-198175503>ANKRD44 ANKRD44 91526 ENSG00000065413 Q8N8A2 chr22.20093700-20093800>DGCR8 DGCR8 54487 ENSG00000128191 Q8WYQ5 chr1.112991564-112991794>CTTNBP2NL CTTNBP2NL 55917 ENSG00000143079 Q9P2B4 chr1.19470474-19470585>UBR4 UBR4 23352 ENSG00000127481 Q5T4S7 chr5.134343647- PCBD2 and 84105 and 347732 ENSG00000132570 and Q9H0N5 and Q86XQ3 134343829>PCBD2andCATSPER3 CATSPER3 ENSG00000152705 chr19.49314066-49314178>BCAT2 BCAT2 587 ENSG00000105552 O15382 chr2.118864235-118864479>INSIG2 INSIG2 51141 ENSG00000125629 Q9Y5U4 chr18.48443613-48443878>ME2 ME2 4200 ENSG00000082212 P23368 chr22.45254869-45255776>PRR5-ARHGAP8 PRR5-ARHGAP8 553158 ENSG00000248405 B1AHC4 chr1.27431807-27432578>SLC9A1 SLC9A1 6548 ENSG00000090020 P19634 chr8.133984843-133984986>TG TG 7038 ENSG00000042832 P01266 41751976>PRICKLE4andTOMM6 PRICKLE4 and 29964 and ENSG00000124593 and Q2TBC4 and Q96649 TOMM6 100188893 ENSG00000214736 chr17.57728564-57728677>CLTC CLTC 1213 ENSG00000141367 Q00610 chr3.150280329-150280447>EIF2A EIF2A 83939 ENSG00000144895 Q9BY44 chr2.242282407-242282508>SEPT2 SEPT2 4735 ENSG00000168385 Q15019 chr21.40619627-40619758>BRWD1 BRWD1 54014 ENSG00000185658 Q9NSI6 chr1.26799700-26800018>HMGN2 HMGN2 3151 ENSG00000198830 P05204 chr5.140895496-140896575>DIAPH1 DIAPH1 1729 ENSG00000131504 O60610 chr5.140895875-140896575>DIAPH1 DIAPH1 1729 ENSG00000131504 O60610 chr1.180049625-180049796>CEP350 CEP350 9857 ENSG00000135837 Q5VT06 chr1.180049652-180049796>CEP350 CEP350 9857 ENSG00000135837 Q5VT06 chr5.70531277-70532281>goychyby goychyby “NoInfo” “NoInfo” “NoInfo” chr13.100543572-100543866>CLYBL CLYBL 171425 ENSG00000125246 Q8NOX4 chr19.36515246-36515534>CLIP3 CLIP3 25999 ENSG00000105270 Q96DZ5 chr6.144289727- PLAGL1 and HYMAI 5325 and 57061 ENSG00000118495 and Q9UM63 and “NoInfo” 144290115>PLAGL1andHYMAI “NoInfo” chr21.47608408-47608855>klorley klorley “NoInfo” “NoInfo” “NoInfo” chr9.17135038-17135423>CNTLN CNTLN 54875 ENSG00000044459 Q9NXGO chr1.114499947-114500540>wawleybo wawleybo “NoInfo” “NoInfo” “NoInfo” chr17.18486655-18486837>CCDC1446 CCDC1446 284047 ENSG00000154874 Q3MJ40 chr4.40800804-40800921>NSUN7 NSUN7 79730 ENSG00000179299 Q8NE18 chr3.39162488-39162680>TTC21A TTC21A 199223 ENSG00000168026 Q8NDW8 chr1.161196029-161196394>TOMM40L TOMM40L 84134 ENSG00000158882 Q969M1 chr7.45083306-45083697>CCM2 CCM2 83605 ENSG00000136280 Q9 BSQ5 chr19.13009896-13010199>SYCE2 SYCE2 256126 ENSG00000161860 Q6PIF2 chr3.20019802-20020396>RABSA RABSA 5868 ENSG00000144566 P20339 chr6.122792844-122793050>SERINC1 SERINC1 57515 ENSG00000111897 Q9NRX5 chr2.231663444-231663879>CAB39 CAB39 51719 ENSG00000135932 Q9Y376 chr1.145790974-145791170>GPR89A GPR89A 653519 ENSG00000117262 B7ZAQ6 chr4.175223190-175223337>KIAA1712 K1AA1712 (CEP44) 80817 ENSG00000164118 Q9C0F1 chr2.182339687-182340015>ITGA4 ITGA4 3676 ENSG00000115232 P13612 chr16.18799866- ARL6IP1 and RPS15A 23204 and 6210 ENSG00000170540 and Q15041 and P62244 18800440>ARL6IP1andRPS15A ENSG00000134419 chr6.3021094-3022352>teyvybo teyvybo “NoInfo” “NoInfo” “NoInfo” chr16.22277711-22277845>EEF2K EEF2K 29904 ENSG00000103319 O00418 chr11.7479027-7479174>veemee veemee “NoInfo” “NoInfo” “NoInfo” chrX.77303661-77305892>ATP7A ATP7A 538 ENSG00000165240 Q04656 chr1.78207302-78207433>USP33 USP33 23032 ENSG00000077254 Q8TEY7 chrX.76776266-76776394>ATRX ATRX 546 ENSG00000085224 P46100 chr12.6761437-6761584>ING4 ING4 51147 ENSG00000111653 Q9UNL4 chr17.77079383-77079672>ENGASE ENGASE 64772 ENSG00000167280 Q8NFI3 chr11.111889680-111893374>DIXDC1 DIXDC1 85458 ENSG00000150764 Q155Q3 chr11.111889680-111893310>DIXDC1 DIXDC1 85458 ENSG00000150764 Q155Q3 chr4.157731989-157732169>PDGFC PDGFC 56034 ENSG00000145431 Q9NRA1 chr20.18449588-18449705>POLR3F POLR3F 10621 ENSG00000132664 Q9H1D9 chr11.47738539-47739064>FNBP4 FNBP4 23360 ENSG00000109920 Q8N3X1 chr16.30593851-30595166>syrar syrar “NoInfo” “NoInfo” “NoInfo” chr13.41593364-41593568>ELF1 ELF1 1997 ENSG00000120690 P32519 chr22.51221467-51221714>RABL2B RABL2B 11158 ENSG00000079974 Q9UNT1 chr9.33264164-33264493>CHMP5 CHMP5 51510 ENSG00000086065 Q9NZZ3 chr1.154928545- 6464 and 90780 and ENSG00000163348 ENSG00000160691 and Q96AQ6 154928780>SHC1andPYGO2andPBXIP1 SHC1 and PYGO2 and and 57326 P29353 and Q9BRQO and PBXIP1 ENSG00000163346 chr19.1953385-1953505>C19orf34 C19orf34 255193 ENSG00000180846 Q8NCQ2 (CSNK1G2-AS1) chr2.113175261-113175491>RGPD8 RGPD8 727851 ENSG00000169629 O14715 chr1.145509166-145509612>RBM8A.1 RBM8A.1 “NoInfo” “NoInfo” “NoInfo” chr1.89271574-89271700>PKN2 PKN2 5586 ENSG00000065243 Q16513 chr10.99433338- DHDPSL (HOGA1) 112817 and 55361 ENSG00000241935 and Q86XE5 and Q9BTU6 99433902>DHOPSLandP14K2A and PI4K2A ENSG00000155252 chr7.74166365-74166897>GTF2I GTF2I 2969 ENSG00000077809 P78347 chr18.54318248-54318824>TXNL1 TXNL1 9352 ENSG00000091164 O43396 chr12.58345541-58345678>XRCC6BP1 XRCC6BP1 91419 ENSG00000166896 Q9Y6H3 chr7.76870183-76870364>CCDC146 CCDC146 57639 ENSG00000135205 Q81YE0 chr3.52385978-52386119>DNAH1 DNAH1 25981 ENSG00000114841 Q9P2D7 chr12.96258857-96259166>SNRPF SNRPF 6636 ENSG00000139343 P62306 chr1.63269390-63269533>ATG4C ATG4C 84938 ENSG00000125703 Q96DT6 chr2.172848099-172848599>HAT1 HAT1 8520 ENSG00000128708 O14929 chr18.67508480-67516323>DOK6 DOK6 220164 ENSG00000206052 Q6PKX4 chr8.30948350-30948458>WRN WRN 7486 ENSG00000165392 Q14191 chr2.208446079-208446884>FAM119A FAM119A 151194 ENSG00000144401 Q8WX61 (METTL21A) chr7.5938415-5938550>CCZ1 CCZ1 51622 ENSG00000122674 P86791 chr19.44619641-44619995>ZNF225 ZNF225 7768 ENSG00000256294 Q9UK10 chr1.243652316-243652442>SDCCAG8 SDCCAG8 10806 ENSG00000054282 Q86SQ7 chr4.122723829-122723983>EXOSC9 EXOSC9 5393 ENSG00000123737 Q06265 chr4.122723829-122723948>EXOSC9 EXOSC9 5393 ENSG00000123737 Q06265 chr1.46805848-46806591>NSUN4andFAAH NSUN4 and FAAH 387338 and 2166 ENSG00000117481 and Q96C69 and 000519 ENSG00000117480 chr10.51592090-51592619>LOC100287554 LOC100287554 “NoInfo” “NoInfo” “NoInfo” chrX.138864706-138864887>ATP11C ATP11C 286410 ENSG00000101974 Q8NB49 chr14.50246313-50246524>KLHDC2 KLHDC2 23588 ENSG00000165516 Q9Y2U9 chr7.22980878-22987334>FAM126A FAM126A 84668 ENSG00000122591 Q9BYI3 chr1.150778337-150778492>CTSK CTSK 1513 ENSG00000143387 P43235 chr12.48094974-48095387>RPAP3 RPAP3 79657 ENSG00000005175 Q9H6T3 chr15.38619054-38620016>koyzawbu koyzawbu “NoInfo” “NoInfo” “NoInfo” chr11.836251-836525>CD151 CD151 977 ENSG00000177697 P48509 chr17.27581220-27581513>CRYBA1 CRYBA1 1411 ENSG00000108255 P05813 chr14.105236090-105236707>AKT1 AKT1 207 ENSG00000142208 P31749 chr10.69828759-69829524>HERC4 HERC4 26091 ENSG00000148634 Q5GLZ8 chr22.50320903-50321181>CRELD2 CRELD2 79174 ENSG00000184164 Q6UXH1 chr12.10561988-10562183>KLRC4andKLRK1 KLRC4 and KLRK1 8302 and 22914 ENSG00000183542 and O43908 and P26718 ENSG00000213809 chr8.104455023-104455428>DCAF13 DCAF13 25879 ENSG00000164934 Q9NVO6 chr12.40441853-40442012>SLC2A13 SLC2A13 114134 ENSG00000151229 Q96QE2 chrX.16870674-16871149>RBBP7 RBBP7 5931 ENSG00000102054 Q16576 chr12.54789679-54790160>ITGA5 ITGA5 3678 ENSG00000161638 P08648 chr1.150939858-150940190>LASS2 LASS2 (CERS2) 29956 ENSG00000143418 Q96G23 chr13.113864293-113864812>PCID2 PCID2 55795 ENSG00000126226 Q5JVF3 chr15.80191177-80191467>ST20andMTHFS ST20 and MTHFS 400410 and 10588 ENSG00000180953 and Q9HBF5 and P49914 ENSG00000136371 chr5.145493406-145493874>LARS LARS 51520 ENSG00000133706 Q9P2J5 chr16.3493611- ZNF174 and NAT15 7727 and 79903 ENSG00000103343 and Q15697 and Q9H7X0 3493837>ZNF174andNAT15andCLUAP1 (NAA60) and CLUAP1 and 23059 ENSG00000122390 and and Q96AJ1 ENSG00000103351 chr6.79664949-79665569>PHIPandTRNAF13P PHIP and TRNAF13P 55023 and ENSG00000146247 and Q8WWQ0 and “NoInfo” 100189446 “NoInfo” chr17.62745780-62746126>LOC146880 LOC146880 146880 ENSG00000215769 “NoInfo” chr17.61473104-61473289>TANC2 TANC2 26115 ENSG00000170921 Q9HCD6 chr15.59102429-59102587>FAM636 FAM636 54629 ENSG00000128923 Q8NBR6 chr10.11272033-11272456>CELF2 CELF2 10659 ENSG00000048740 O95319 chr20.34487292-34487561>PHF20 PHF20 51230 ENSG00000025293 Q9BVI0 chr8.74858684-74859055>TCEB1 TCEB1 6921 ENSG00000154582 Q15369 chr2.17953901-17954051>GEN1 GEN1 348654 ENSG00000178295 Q17RS7 chr14.88431849-88431973>GALC GALC 2581 ENSG00000054983 P54803 chr19.1877203-1877424>FAM108A1 FAM108A1 81926 ENSG00000129968 Q96GS6 (ABHD17A) chr17.18087711-18088067>jeeroy jeeroy “NoInfo” “NoInfo” “NoInfo” chr1.168262382- SFT2D2 and TBX19 375035 and 9095 ENSG00000213064 and O95562 and O60806 168262516>SFT2D2andTBX19 ENSG00000143178 chr6.158088239-158089557>fyjaw fyjaw “NoInfo” “NoInfo” “NoInfo” chr15.30711214-30711348>rukaru rukaru “NoInfo” “NoInfo” “NoInfo” chr8.24256387-24256553>ADAMDEC1 ADAMDEC1 27299 ENSG00000134028 O15204 chr15.57545460-57545666>stoyguby stoyguby “NoInfo” “NoInfo” “NoInfo” chr10.75230828-75230967>PPP3CB PPP3CB 5532 ENSG00000107758 P16298 chr20.43808628-43808775>rotora rotora “NoInfo” “NoInfo” “NoInfo” chr1.46467098-46468407>MAST2 MAST2 23139 ENSG00000086015 Q6P0Q8 chr7.2635311-2636062>dochuby dochuby “NoInfo” “NoInfo” “NoInfo” chr19.11411543-11411912>tojaw tojaw “NoInfo” “NoInfo” “NoInfo” chrX.153744234-153744566>FAM3A FAM 3A 60343 ENSG00000071889 P98173 chr2.73957016-73957156>TPRKB TPRKB 51002 ENSG00000144034 Q9Y3C4 chr2.234112772-234113219>INPP5D INPP5D 3635 ENSG00000168918 Q92835 chr6.41036580- C6orf130 (OARD1) 221443 and 222643 ENSG00000124596 and Q9Y530 and Q8IV45 41036692>C6orf130andUNC5CL and UNC5CL ENSG00000124602 chr15.75165540-75165688>SCAMP2 SCAMP2 10066 ENSG00000140497 O15127 chrX.74282163-74282417>ABCB7 ABCB7 22 ENSG00000131269 O75027 chr2.88336462-88336570>KRCC1 KRCC1 51315 ENSG00000172086 Q9NPI7 chrX.2839944-2840065>ARSD ARSD 414 ENSG00000006756 P51689 chr11.89933252-89935719>CHORDC1 CHORDC1 26973 ENSG00000110172 Q9UHD1 chr8.62438536-62438671>ASPH ASPH 444 ENSG00000198363 Q12797 chr3.69028819-69028938>C3orf64 C3orf64 (EOGT) 285203 ENSG00000163378 Q5NDL2 chr5.35053745-35054334>fugey fugey “NoInfo” “NoInfo” “NoInfo” chr9.35737655-35737936>GBA2 GBA2 57704 ENSG00000070610 Q9HCG7 chr15.94774950-94775234>MCTP2 MCTP2 55784 ENSG00000140563 Q6DN12 chr3.52561845-52561947>NT5DC2 NT5DC2 64943 ENSG00000168268 Q9H857 chr1.85039599-85040103>CTBSandGNG5 CTBS and GNG5 1486 and 2787 ENSG00000117151 and Q01459 and P63218 ENSG00000174021 chr10.99195666-99196308>EXOSC1 EXOSC1 51013 ENSG00000171311 Q9Y3B2 chr20.23401942-23402097>NAPB NAPB 63908 ENSG00000125814 Q9H115 chr17.36351796-36351996>TBC1D3 TBC1D3 729873 ENSG00000197681 Q8IZP1 chrX.118985730-118985836>UPF3B UPF3B 65109 ENSG00000125351 Q9BZI7 chr15.66811217-66811416>ZWILCH ZWILCH 55055 ENSG00000174442 Q9H900 chr15.66811217-66811467>ZWILCH ZWILCH 55055 ENSG00000174442 Q9H900 chr11.125490667- STT3A and CHEK1 3703 and 1111 ENSG00000134910 and P46977 and O14757 125490901>STT3AandCHEK1 ENSG00000149554 chr3.15778540-15778740>ANKRD28 ANKRD28 23243 ENSG00000206560 O15084 chr19.9720432-9722012>ZNF562andZNF561 ZNF562 and ZNF561 54811 and 93134 ENSG00000171466 and Q6V9R5 and Q8N587 ENSG00000171469 chr3.167452594-167452717>PDCD10 PDCD10 11235 ENSG00000114209 Q9BUL8 chr1.10509776-10510379>APITD1andCORT APITD1 and CORT 378708 and 1325 ENSG00000175279 and Q8N2Z9 and O00230 ENSG00000241563 chr6.34360041-34360260>RPS10andNUDT3 RPS10 and NUDT3 6204 and 11165 ENSG00000124614 and P46783 and O95989 ENSG00000272325 chr19.52207575-52207733>NCRNA00085 NCRNA00085 147650 ENSG00000182310 No Data (SPACA6P) chr11.62105383-62105784>saroro saroro “NoInfo” “NoInfo” “NoInfo” chr1.17056-17742>WASH7P WASH7P 653635 ENSG00000227232 NoData chr1.45987501-45987609>PRDX1 PRDX1 5052 ENSG00000117450 Q06830 chr1.243419358-243419542>SDCCAG8 SDCCAG8 10806 ENSG00000054282 Q86SQ7 chr2.111302237-111302383>RGPD6 RGPD6 729540 ENSG00000183054 Q99666 chr2.110584278-110584424>RGPD5 RG PDS 84220 ENSG00000015568 Q99666 chr6.109248281-109249436>ARMC2 ARMC2 84071 ENSG00000118690 Q8NENO chr14.96997812-96999040>PAPOLA PAPOLA 10914 ENSG00000090060 P51003 chr19.58423428- ZNF417 and ZNF814 147687 and 730051 ENSG00000173480 and Q8TAU3 and B7Z6K7 58423554>ZNF417andZNF814 ENSG00000204514 chr19.58423428- ZNF417 and ZNF814 147687 and 730051 ENSG00000173480 and Q8TAU3 and B7Z6K7 58423557>ZNF417andZNF814 ENSG00000204514 chrX.149924161-149924396>MTMR1 MTM R1 8776 ENSG00000063601 Q13613 chr19.5208248-5208402>PTPRS PTPRS 5802 ENSG00000105426 Q13332 chr14.20872770-20872931>TEP1 TEP1 7011 ENSG00000129566 Q99973 chr20.416929-419485>TBC1D20 TBC1D20 128637 ENSG00000125875 Q966Z9 chr15.59943710-59944525>GTF2A2 GTF2A2 2958 ENSG00000140307 P52657 chrX.15862547-15863639>AP1S2 AP1S2 8905 ENSG00000182287 P56377 chr15.64017491-64017712>HERC1 HERC1 8925 ENSG00000103657 Q15751 chr5.77656415-77656552>SCAMP1 SCAMP1 9522 ENSG00000085365 O15126 chr19.47646729-47646862>SAE1 SAE1 10055 ENSG00000142230 Q9UBE0 chr19.47646751-47646862>SAE1 SAE1 10055 ENSG00000142230 Q9UBE0 chr3.81552424-81552865>chordybo chordybo “NoInfo” “NoInfo” “NoInfo” chr1.201780731-201780885>NAV1 NAV1 89796 ENSG00000134369 Q8NEY1 chr11.61129205-61129720>CYBASC3 CYBASC3 220002 ENSG00000162144 Q8NBI2 (CYB561A3) chr11.6523983-6524156>FXC1 andDNHID1 FXC1 (TIMM10B) 26515 and 144132 ENSG00000132286 and Q9Y5J6 and Q96M86 and DNHD1 ENSG00000179532 chr19.8441789-8441951>lyta lyta “NoInfo” “NoInfo” “NoInfo” chr6.153291674-153292549>FBX05 FBX05 26271 ENSG00000112029 Q9UKT4 chr6.153291660-153292549>FBX05 FBX05 26271 ENSG00000112029 Q9UKT4 chr6.153291654-153292549>FBX05 FBX05 26271 ENSG00000112029 Q9UKT4 chr7.29549802-29552165>klerky klerky “NoInfo” “NoInfo” “NoInfo” chr22.41175013-41175129>SLC25A17 SLC25A17 10478 ENSG00000100372 O43808 chr4.76874494-76874938>sporsmorby sporsmorby “NoInfo” “NoInfo” “NoInfo” chr5.39274505-39274630>FYB FYB 2533 ENSG00000082074 O15117 chr10.32324818-32324922>KIF5B KIF5B 3799 ENSG00000170759 P33176 chr14.52957557-52957723>TXNDC16 TXNDC16 57544 ENSG00000087301 Q9P2K2 chr14.88452833-88452946>GALC GALC 2581 ENSG00000054983 P54803 chr20.30720816-30720929>TM9SF4 TM9SF4 9777 ENSG00000101337 Q92544 chr19.54610118-54610266>NDUFA3 NDUFA3 4696 ENSG00000170906 095167 chr10.92500578-92502285>HTR7 HTR7 3363 ENSG00000148680 P34969 chr3.25637911-25639423>RARB RABB 5915 ENSG00000077092 P10826 chr5.14381239-14381361>TRIO TRIO 7204 ENSG00000038382 O75962 chr2.243168539-243168819>samemo samemo “NoInfo” “NoInfo” “NoInfo” chr3.137963865-137964523>vusmyby vusmyby “NoInfo” “NoInfo” “NoInfo” chr3.137963930-137964523>ARMC8 ARMC8 25852 ENSG00000114098 Q8IUR7 chr3.137963930-137964524>ARMC8 ARMC8 25852 ENSG00000114098 Q8IUR7 chr14.100743755-100744113>YY1 YY1 7528 ENSG00000100811 P25490 Table 1E—Exon Usage Upregulated in Subjects Who Have Not Experienced ischemic Stroke/ICH chr20.32880178-32880359>AHCY AHCY 191 ENSG00000101444 P23526 chr2.242611606-242612016>ATG4B ATG4B 23192 ENSG00000168397 Q9Y4P1 chr9.96866557-96866667>PTPDC1 PTPDC1 138639 ENSG00000158079 A2A3K4 chr17.42982993-42984756>GFAP GFAP 2670 ENSG00000131095 P14136 chr22.41252435-41253036>ST13 ST13 6767 ENSG00000100380 P50502 chr1.53416427-53416558>SCP2 SCP2 6342 ENSG00000116171 P22307 chr6.32806430-32806547>TAP2andHLA-DOB TAP2 and HLA-DOB 6891 and 3112 ENSG00000204267 and Q03519 and P13765 ENSG00000241106 chr14.19683027-19683434>DUXAP10 DUXAP10 503639 ENSG00000257227 “NoInfo” chr9.95018962-95019082>IARS IARS 3376 ENSG00000196305 P41252 chr19.39138368-39138547>ACTN4 ACTN4 81 ENSG00000130402 O43707 chr9.140473077-140473340>WDR85 WDR85 (DPH7) 92715 ENSG00000148399 Q9BTV6 chrX.48367956-48368344>PORCN PORCN 64840 ENSG00000102312 Q9H237 chr2.101606718-101606908>NPAS2 NPAS2 4862 ENSG00000170485 Q99743 chr7.101475858-101476865>snorkar snorkar “NoInfo” “NoInfo” “NoInfo” chr19.45543176-45543569>SFRS16 SFRS16 (CLASRP) 11129 ENSG00000104859 Q8N2M8 chr18.28642978-28643439>DSC2 DSC2 1824 ENSG00000134755 Q02487 chr22.36892014- FOXRED2 and TXN2 80020 and 25828 ENSG00000100350 and Q8IWF2 and Q99757 36892255>FOXRED2andTXN2 ENSG00000100348 chr18.43417478-43417850>SIGLEC15 SIGLEC15 284266 ENSG00000197046 Q6ZMC9

TABLE 7 Differential Exon Usage in the 5 Groups (p < 0.005, FC > |1.21|). FC—Fold Change CE Stroke vs. CE Stroke vs. CE Stroke vs. CE Stroke vs. Controls ICH LV Lacunar Upregulated in CE IS p- p- p- p- Marker ID Gene Symbol value FC value FC value FC value FC chr1.86861716-86861978 > ODF2L ODF2L 4.89E−04 32.54 8.33E−02 1.68 4.39E−04 52.79 4.15E−04 77.95 chr10.38299602-38299711 > ZNF33A ZNF33A 1.34E−03 8.75 4.81E−04 >500 3.54E−03 4.52 4.80E−04 Not Esti- mable chr10.38299604-38299711 > ZNF33A ZNF33A 1.34E−03 8.75 4.81E−04 >500 3.54E−03 4.52 4.80E−04 Not Esti- mable chr10.49253461-49254183 > BMS1P7 BMS1P7 3.00E−04 11.83 1.29E−04 >500 2.16E−03 3.62 5.90E−04 6.62 chr14.70242552-70243105 > SLC10A1 SLC10A1 3.87E−04 Not 1.52E−02 2.52 4.05E−03 3.93 7.65E−03 3.10 Esti- mable chr17.34856670-34856799 > MYO19 MYO19 6.48E−04 7.89 2.45E−03 3.85 1.19E−03 5.32 4.55E−04 11.01 chr17.73000302-73002233 > CDR2L CDR2L 1.76E−05 10.40 1.03E−05 19.45 1.19E−05 15.70 2.54E−05 7.93 chr19.18959976-18960255 > UPF1 UPF1 6.28E−04 4.27 8.00E−05 21.25 4.87E−05 Not 9.17E−05 16.73 Esti- mable chr19.58427747-58427959 > ZNF417 and 4.40E−04 4.45 3.91E−02 1.64 5.11E−05 31.22 4.31E−05 62.20 ZNF417andZNF814 ZNF814 chr19.58427747-58427960 > ZNF417 and 4.40E−04 4.45 3.91E−02 1.64 5.11E−05 31.22 4.31E−05 62.20 ZNF417andZNF814 ZNF814 chr2.119988299-119988610 > STEAP3 STEAP3 4.66E−04 199.47 1.78E−03 6.53 4.46E−04 >500 5.08E−04 68.51 chr2.179463448-179463831 > CCDC141 and 4.17E−06 56.83 5.56E−05 4.49 3.38E−06 >500 3.38E−06 >500 CCDC141andTTN TTN chr2.25258142-25260098 > LOC729723 LOC729723 1.67E−03 4.92 4.83E−04 13.26 6.86E−04 8.95 5.62E−04 10.97 chr20.43995515-43996064 > SYS1-DBNDD2 SYS1- 1.17E−02 9.29 9.88E−02 2.21 2.68E−02 −1.76 3.16E−02 3.81 DBNDD2 chr22.19115606-19115962 > skatee skatee 1.69E−02 1.83 6.02E−04 3.72 5.45E−05 16.63 2.53E−04 5.12 chr3.188326949-188327339 > LPP LPP 1.18E−03 9.73 6.73E−04 24.42 5.40E−04 61.39 4.89E−04 196.57 chr3.48456585-48456756 > PLXNB1 PLXNB1 1.81E−05 Not 3.29E−04 4.01 1.81E−05 >500 7.19E−04 3.20 Esti- mable chr3.49448633-49449166 > myforbo myforbo 3.99E−04 5.56 2.06E−04 8.39 8.58E−02 1.50 1.01E−04 19.14 chr4.15570247-15570813 > klawgu klawgu 3.67E−04 7.05 8.78E−03 2.30 6.85E−02 1.58 5.41E−04 5.61 chr6.37225553-37225749 > TBC1D22B TBC1D22B 2.24E−01 1.22 2.12E−02 1.59 1.12E−01 −1.24 7.61E−04 2.56 chr7.142630429-142630905 > TRPV5 TRPV5 1.01E−03 4.98 4.08E−03 2.99 1.34E−04 >500 1.68E−04 42.44 chr7.158334118-158334468 > PTPRN2 PTPRN2 1.50E−04 Not 2.64E−04 17.40 3.29E−03 3.27 2.01E−04 33.34 Esti- mable chr8.104406853-104407319 > shuskeebu shuskeebu 9.62E−05 18.92 4.82E−03 2.47 2.53E−04 7.00 1.48E−03 3.32 ICH CE Stroke vs. Controls vs. vs. LV LV LV LV vs. Lacunar Upregulated in LV IS p- p- p- p- Marker ID Gene Symbol value FC value FC value FC value FC chr1.214836934-214837426 > CENPF 5.00E−04 −3.69 5.93E−02 −1.51 1.21E−03 −2.91 1.98E−04 5.17 CENPF chr10.46918169-46918362 > FAM35B and 1.26E−02 −2.69 2.31E−03 −5.33 4.16E−04 <−500 7.30E−04 16.07 FAM35BandRHEBP1 RHEBP1 chr11.62389338-62389648 > B3GAT3 2.98E−04 −184.49 1.74E−03 −5.23 1.16E−02 −2.57 3.51E−03 3.78 B3GAT3 chr12.54645834-54646011 > CBX5 CBX5 4.19E−04 −9.67 1.51E−04 <−500 1.53E−04 <−500 7.79E−04 6.06 chr12.56334947-56335109 > DGKA DGKA 3.08E−02 −2.03 3.68E−03 −3.73 4.70E−04 −19.19 9.49E−04 7.91 chr13.103506107-103506222 > BIVM and 3.55E−07 −8.46 1.47E−07 −18.25 7.87E−08 −119.86 1.72E−07 15.06 BIVMandERCC5 ERCC5 chr14.53248502-53248629 > GNPNAT1 3.32E−03 −3.53 2.07E−04 <−500 4.12E−04 −13.92 4.11E−02 1.85 GNPNAT1 chr15.101847418-101849508 > PCSK6 2.64E−05 −9.47 1.70E−04 −3.93 1.94E−03 −2.29 1.42E−05 18.68 PCSK6 chr15.81584265-81585378 > IL16 IL16 4.03E−04 −7.21 1.56E−02 −2.08 1.94E−03 −3.49 1.93E−04 14.76 chr16.4475881-4476093 > DNAJA3 DNAJA3 4.39E−04 −9.19 2.89E−01 −1.28 2.48E−02 −1.98 3.13E−03 3.32 chr16.72146312-72146549 > DHX38 DHX38 3.43E−04 <−500 3.58E−04 −207.50 6.13E−04 −15.82 3.43E−04 >500 chr17.43002077-43003867 > KIF18B KIF18B 7.66E−04 −4.84 4.20E−04 −6.67 3.80E−02 −1.75 2.95E−03 3.02 chr2.173420100-173420447 > PDK1 PDK1 5.32E−04 −8.27 6.79E−03 −2.69 2.85E−03 −3.49 3.74E−04 11.68 chr2.20756227-20757428 > dawgorbu 5.41E−04 −3.87 2.90E−05 Not 2.42E−04 −5.27 1.12E−04 8.19 dawgorbu Estimable chr20.33056659-33057236 > vytaw vytaw 3.05E−04 −11.22 2.33E−03 −3.50 7.30E−04 −5.73 1.25E−04 Not Esti- mable chr20.43995515-43996064 > SYS1- SYS1- 2.68E−02 −1.76 8.54E−05 −16.38 7.51E−04 −3.90 2.23E−04 6.72 DBNDD2 DBNDD2 chr20.52560545-52561535 > BCAS1 BCAS1 1.65E−04 −247.51 3.31E−03 −3.31 6.66E−04 −6.90 3.85E−04 11.11 chr22.18613610-18614498 > PEX26 and 1.36E−02 −2.14 3.42E−04 −8.12 9.20E−04 −4.61 7.57E−02 1.57 PEX26andTUBA8 TUBA8 chr22.29141852-29141989 > HSCB HSCB 4.31E−03 −3.84 9.81E−03 −2.87 4.12E−04 −167.51 2.88E−03 4.61 chr3.49448633-49449166 > myforbo myforbo 8.58E−02 1.50 1.68E−02 −3.71 8.50E−03 −5.60 3.98E−03 12.77 chr3.8606070-8609805 > LMCD1 LMCD1 6.35E−03 −3.28 2.63E−03 −4.75 1.48E−03 −6.74 3.77E−04 Not Esti- mable chr4.15570247-15570813 > klawgu klawgu 6.85E−02 1.58 1.98E−02 −4.45 3.12E−01 −1.45 2.90E−02 3.54 chr5.162902464-162902678 > HMMR 2.07E−04 <−500 1.05E−03 −5.96 1.57E−03 −4.80 4.74E−03 3.13 HMMR chr5.176715528-176715926 > NSD1 NSD1 3.78E−04 −8.90 1.22E−04 Not 1.01E−03 −4.81 3.10E−04 10.77 Estimable chr5.61688639-61688817 > DIMT1L DIMT1L 1.15E−03 −4.55 2.66E−04 −12.85 5.61E−03 −2.70 1.79E−04 26.01 chr6.100023529-100023947 > RPS3P5 6.84E−05 −7.70 2.96E−05 −17.42 1.92E−04 −4.63 4.47E−05 10.72 RPS3P5 chr6.111619174-111619773 > slyjey slyjey 6.80E−05 −6.99 4.07E−04 −3.47 1.65E−02 −1.74 2.30E−05 19.83 chr6.37225553-37225749 > TBC1D22B 1.12E−01 −1.24 9.78E−03 −1.52 6.80E−04 −1.98 2.94E−05 3.18 TBC1D22B chr7.2282560-2282683 > NUDT1 NUDT1 5.87E−04 −3.95 3.45E−05 Not 3.70E−05 −150.96 1.65E−04 7.00 Estimable chr8.90798887-90799401 > RIPK2 RIPK2 1.00E−04 −18.86 1.65E−04 −10.01 3.30E−02 −1.74 4.32E−04 5.31 chr9.131486273-131486409 > ZDHHC12 1.41E−05 −6.54 2.13E−05 −5.43 5.90E−06 −11.68 8.83E−06 8.53 ZDHHC12 chrX.152226503-152227128 > PNMA3 3.13E−03 −4.43 4.20E−04 −126.98 5.52E−04 −26.32 1.74E−03 6.14 PNMA3 CE Stroke vs. Controls vs. ICH vs. Upregulated in Lacunar IS Lacunar Lacunar Lacunar LV vs. Lacunar Gene p- p- p- p- Marker ID Symbol value FC value FC value FC value FC chr1.155691308-155691471 > DAP3 1.44E−03 −5.83 1.51E−02 −2.40 4.78E−04 −18.04 9.64E−04 −7.72 DAP3 chr1.160580214-160580588 > SLAMF1 9.00E−05 −50.28 6.08E−04 −4.99 8.40E−05 −75.82 1.30E−04 −17.92 SLAMF1 chr1.246729640-246730091 > CNST 1.49E−04 <−500 1.49E−04 <−500 5.30E−04 −7.83 1.12E−02 −2.35 CNST chr11.119039480-119040011 > NLRX1 2.47E−03 −4.13 8.08E−04 −7.84 5.40E−04 −11.67 3.97E−04 −18.66 NLRX1 chr11.62475067-62475387 > GNG3 2.61E−02 −2.07 2.51E−04 <−500 8.27E−03 −2.76 6.18E−04 −10.50 GNG3 chr12.111065735-111066029 > TCTN1 2.36E−04 <−500 5.53E−04 −11.15 2.41E−04 −407.21 2.36E−04 <−500 TCTN1 chr12.123262038-123262230 > CCDC62 7.34E−03 −3.02 6.85E−04 −12.40 1.61E−03 −5.83 4.55E−04 −27.30 CCDC62 chr12.2966630-2968829 > FOXM1 4.11E−04 −4.71 9.88E−04 −3.47 2.51E−03 −2.72 1.60E−04 −7.77 FOXM1 chr12.94914730-94915694 > LOC400061 8.26E−04 −2.46 2.57E−01 −1.20 1.49E−05 −9.38 4.11E−06 Not LOC400061 Estimable chr14.96795821-96795971 > ATG2B 1.42E−04 −4.39 5.92E−04 −2.96 1.69E−02 −1.70 6.23E−05 −6.19 ATG2B chr15.52970203-52970319 > KIAA1370 7.48E−02 −1.68 2.15E−02 −2.19 2.45E−03 −4.32 2.70E−04 <−500 KIAA1370 chr16.15013757-15013940 > zoner zoner 8.81E−03 −2.19 3.72E−02 −1.70 2.46E−03 −2.90 5.61E−05 Not Estimable chr18.33077683-33077895 > INO80C 1.26E−03 −4.39 3.20E−04 −10.51 6.38E−02 −1.64 2.82E−03 −3.28 INO80C chr19.35173682-35173954 > ZNF302 5.42E−04 −24.66 7.08E−04 −14.32 4.23E−04 −74.20 4.45E−04 −52.73 ZNF302 chr2.101627502-101628002 > TBC1D8 2.60E−04 −13.65 1.09E−03 −4.69 1.25E−04 <−500 3.07E−04 −11.16 TBC1D8 chr2.160143094-160143317 > WDSUB1 1.02E−03 −8.14 3.24E−04 Not 6.23E−03 −3.18 2.45E−03 −4.63 WDSUB1 Estimable chr2.29258330-29258510 > FAM179A 2.28E−05 <−500 7.40E−05 −9.36 5.57E−05 −12.23 4.93E−03 −2.20 FAM179A chr20.32079185-32079982 > spawvor 1.44E−05 Not 1.47E−04 −5.01 3.41E−04 −3.73 6.92E−05 −7.31 spawvor Estimable chr21.47706315-47706712 > C21orf57 3.23E−05 −21.91 9.74E−05 −7.03 1.42E−04 −5.74 1.96E−05 −2028.81 C21orf57 chr22.24316496-24316679 > GSTTP1 and 4.42E−03 −3.29 7.91E−04 −7.77 9.06E−02 −1.60 4.00E−04 −17.20 GSTTP1andDDT DDT chr22.44514918-44515020 > PARVB 3.20E−03 −3.27 6.91E−04 −6.35 4.81E−02 −1.74 2.99E−04 −13.44 PARVB chr5.156821041-156822687 > ADAM19 3.01E−04 −16.01 2.15E−02 −2.06 1.13E−03 −5.14 2.42E−03 −3.71 ADAM19 chr6.146285293-146285525 > SHPRH 8.44E−04 −4.84 3.55E−04 −8.05 4.01E−02 −1.75 2.61E−04 −10.55 SHPRH chr6.146285293-146285559 > SHPRH 8.44E−04 −4.84 3.55E−04 −8.05 4.01E−02 −1.75 2.61E−04 −10.55 SHPRH chr6.163984476-163984751 > QKI QKI 3.99E−07 −5.23 6.22E−08 −15.32 7.43E−07 −4.34 2.09E−07 −6.72 chr6.168370462-168372588 > MLLT4 7.37E−03 −2.24 9.05E−04 −3.79 2.40E−03 −2.86 4.22E−04 −5.10 MLLT4 chr6.30610545-30612432 > C6orf134 3.16E−04 −5.69 1.56E−04 −8.92 5.98E−04 −4.30 1.39E−02 −1.97 C6orf134 chr7.99674926-99675056 > ZNF3 ZNF3 6.70E−04 −6.08 4.74E−04 −7.65 9.91E−03 −2.37 2.97E−04 −11.79 chr8.10340434-10340741 > LOC346702 5.43E−05 −6.06 1.95E−05 −12.38 7.60E−06 <−500 1.33E−05 −20.57 LOC346702 chr9.46687439-46688197 > KGFLP1 1.22E−05 <−500 1.22E−05 <−500 1.22E−05 <−500 3.46E−05 −10.97 KGFLP1 chrX.40495835-40495964 > CXorf38 1.50E−03 −7.97 4.89E−04 Not 5.85E−04 −49.12 5.41E−04 −86.98 CXorf38 Estimable ICH CE Stroke vs. Controls vs. vs. ICH ICH LV ICH vs. Lacunar Upregulated in ICH p- p- p- p- Marker ID Gene Symbol value FC value FC value FC value FC chr1.10509776-10510379 > APITD1 and 7.04E−04 −4.22 4.26E−04 −5.20 1.17E−04 13.61 8.89E−05 20.93 APITD1andCORT CORT chr1.112991564-112991794 > CTTNBP2NL 2.49E−02 −1.96 7.67E−03 −2.53 4.28E−04 8.64 3.22E−03 3.21 CTTNBP2NL chr1.114499947-114500540 > wawleybo 1.41E−01 −1.44 1.46E−03 −4.21 3.22E−04 11.02 8.68E−04 5.33 wawleybo chr1.145509166-145509612 > RBM8A.1 1.52E−03 −4.05 2.57E−03 −3.37 4.91E−04 7.24 3.48E−04 9.57 RBM8A.1 chr1.145790974-145791170 > GPR89A GPR89A 2.08E−04 −9.88 1.17E−02 −2.13 3.99E−02 1.71 1.49E−03 3.53 chr1.150778337-150778492 > CTSK CTSK 6.96E−06 −2.75 1.17E−06 −3.85 5.52E−03 1.44 1.17E−04 1.96 chr1.150939858-150940190 > LASS2 LASS2 3.59E−05 −8.01 6.54E−05 −5.76 9.12E−04 2.65 1.47E−04 4.20 chr1.154928545-154928780 > SHC1 and 3.65E−04 Not 1.55E−03 −6.39 4.42E−03 3.72 1.44E−02 2.53 SHC1andPYGO2andPBXIP1 PYGO2 and Estimable PBXIP1 chr1.161196029-161196394 > TOMM40L 1.18E−02 −2.53 9.42E−04 −7.43 2.63E−04 >500 6.66E−04 10.15 TOMM40L chr1.168262382-168262516 > SFT2D2 and 1.10E−03 −3.16 5.90E−03 −2.19 4.08E−04 4.29 1.13E−04 8.20 SFT2D2andTBX19 TBX19 chr1.17056-17742 > WASH7P WASH7P 7.18E−04 −10.55 1.11E−03 −7.10 4.84E−04 18.86 2.00E−03 4.94 chr1.180049625-180049796 > CEP350 CEP350 1.98E−02 −1.72 9.32E−04 −2.93 2.29E−04 4.37 2.51E−03 2.39 chr1.180049652-180049796 > CEP350 CEP350 1.98E−02 −1.72 9.32E−04 −2.93 2.29E−04 4.37 2.51E−03 2.39 chr1.19470474-19470585 > UBR4 UBR4 4.12E−04 −2.86 8.91E−03 −1.76 2.07E−05 8.19 1.23E−04 3.84 chr1.201780731-201780885 > NAV1 NAV1 6.28E−05 −6.82 1.22E−04 −4.98 4.14E−05 8.94 1.12E−01 1.36 chr1.235956803-235956912 > LYST LYST 4.09E−04 −7.06 9.57E−05 Not 1.31E−01 1.44 1.86E−03 3.52 Estimable chr1.243419358-243419542 > SDCCAG8 3.06E−04 −87.36 2.16E−03 −4.61 1.69E−02 2.32 7.16E−03 2.94 SDCCAG8 chr1.243652316-243652442 > SDCCAG8 1.83E−03 −2.98 1.58E−04 −8.34 6.05E−03 2.28 6.33E−04 4.10 SDCCAG8 chr1.26799700-26800018 > HMGN2 HMGN2 1.04E−03 −2.73 3.52E−05 −10.65 7.29E−05 6.45 1.74E−04 4.42 chr1.27431807-27432578 > SLC9A1 SLC9A1 4.90E−02 −1.58 3.25E−04 −4.86 1.19E−02 1.96 3.45E−03 2.47 chr1.45987501-45987609 > PRDX1 PRDX1 3.62E−06 <−500 1.49E−05 −8.59 9.31E−05 3.89 4.92E−05 4.78 chr1.46467098-46468407 > MAST2 MAST2 3.48E−04 −3.59 1.16E−04 −5.26 5.31E−05 8.00 1.14E−02 1.83 chr1.46805848-46806591 > NSUN4 and 6.05E−05 <−500 1.71E−04 −10.12 1.51E−02 1.99 6.05E−05 >500 NSUN4andFAAH FAAH chr1.63269390-63269533 > ATG4C ATG4C 3.01E−05 −7.06 1.05E−05 −18.05 6.94E−05 4.82 1.23E−05 14.55 chr1.78207302-78207433 > USP33 USP33 1.91E−03 −3.35 4.75E−03 −2.62 1.69E−02 2.01 4.67E−04 5.92 chr1.85039599-85040103 > CTBS and 1.53E−03 −6.62 2.47E−03 −4.94 4.75E−04 42.06 5.65E−04 23.30 CTBSandGNG5 GNG5 chr1.85127881-85128058 > SSX2IP SSX2IP 1.86E−01 −1.31 6.50E−04 −3.62 1.03E−02 1.98 1.57E−04 6.44 chr1.89271574-89271700 > PKN2 PKN2 6.12E−04 −6.28 1.13E−02 −2.29 1.87E−04 23.55 1.20E−03 4.46 chr10.11272033-11272456 > CELF2 CELF2 6.92E−04 −2.68 1.36E−04 −3.96 1.47E−05 13.37 6.22E−05 5.22 chr10.32324818-32324922 > KIF5B KIF5B 2.07E−03 −2.30 1.93E−01 −1.26 2.91E−04 3.49 8.95E−03 1.84 chr10.51592090-51592619 > LOC100287554 9.51E−03 −2.27 4.56E−04 −6.21 1.87E−03 3.42 9.11E−04 4.43 LOC100287554 chr10.69828759-69829524 > HERC4 HERC4 9.83E−04 −5.89 1.21E−02 −2.38 5.78E−04 8.60 1.86E−04 >500 chr10.75230828-75230967 > PPP3CB PPP3CB 8.45E−04 −4.23 4.34E−03 −2.61 2.62E−04 7.78 4.88E−02 1.65 chr10.92500578-92502285 > HTR7 HTR7 8.97E−05 −3.59 5.98E−02 −1.38 3.65E−04 2.65 4.87E−03 1.82 chr10.99195666-99196308 > EXOSC1 EXOSC1 2.77E−04 −36.28 1.45E−02 −2.32 5.19E−04 10.77 2.56E−03 3.92 chr10.99433338-99433902 > DHDPSL and 9.07E−05 −29.65 7.99E−05 −46.47 2.70E−04 7.33 1.53E−04 11.94 DHDPSLandPI4K2A PI4K2A chr11.111889680-111893310 > DIXDC1 1.93E−04 −8.50 6.36E−03 −2.33 1.87E−02 1.90 3.94E−04 5.46 DIXDC1 chr11.111889680-111893374 > DIXDC1 1.93E−04 −8.50 6.36E−03 −2.33 1.87E−02 1.90 3.94E−04 5.46 DIXDC1 chr11.125490667-125490901 > STT3A and 6.31E−08 <−500 7.17E−08 −95.82 6.83E−08 148.17 1.54E−07 14.95 STT3AandCHEK1 CHEK1 chr11.47738539-47739064 > FNBP4 FNBP4 3.24E−04 −10.00 2.29E−03 −3.47 2.00E−04 19.17 1.66E−04 29.34 chr11.61129205-61129720 > CYBASC3 2.94E−04 −16.63 2.29E−04 −28.81 7.91E−04 6.27 1.34E−02 2.28 CYBASC3 chr11.62105383-62105784 > saroro saroro 2.68E−04 <−500 2.68E−04 <−500 2.68E−04 >500 2.68E−04 >500 chr11.6523983-6524156 > FXC1 and 2.16E−04 −20.50 2.28E−03 −3.58 7.96E−04 5.63 1.59E−02 2.15 FXC1andDNHD1 DNHD1 chr11.7479027-7479174 > veemee veemee 5.89E−05 <−500 1.17E−03 −3.62 3.17E−03 2.75 3.03E−04 6.49 chr11.836251-836525 > CD151 CD151 4.18E−05 −7.43 6.65E−05 −5.80 1.16E−05 38.09 1.80E−05 15.64 chr11.89933252-89935719 > CHORDC1 8.39E−05 −12.95 3.53E−04 −4.87 4.83E−03 2.33 1.37E−04 8.21 CHORDC1 chr12.10561988-10562183 > KLRC4 and 2.87E−03 −3.91 8.17E−03 −2.76 1.16E−03 6.12 3.22E−04 33.90 KLRC4andKLRK1 KLRK1 chr12.40441853-40442012 > SLC2A13 SLC2A13 6.39E−05 −5.50 3.03E−05 −8.23 7.21E−06 >500 1.36E−05 18.27 chr12.48094974-48095387 > RPAP3 RPAP3 6.56E−03 −2.64 7.99E−02 −1.59 2.33E−03 3.59 4.90E−04 7.84 chr12.54789679-54790160 > ITGA5 ITGA5 9.53E−03 −2.85 1.58E−03 −6.27 5.00E−04 28.60 5.65E−04 20.66 chr12.58345541-58345678 > XRCC6BP1 4.42E−05 −135.95 1.80E−04 −7.31 1.49E−03 3.11 8.16E−05 15.47 XRCC6BP1 chr12.6761437-6761584 > ING4 ING4 1.90E−05 −4.46 2.22E−04 −2.56 1.61E−03 1.94 4.32E−05 3.55 chr12.96258857-96259166 > SNRPF SNRPF 6.80E−06 −15.03 3.06E−06 <−500 1.16E−05 9.15 3.05E−06 Not Esti- mable chr13.100543572-100543866 > CLYBL CLYBL 1.02E−02 −2.73 8.81E−04 −9.28 3.93E−04 47.46 7.38E−04 11.24 chr13.113864293-113864812 > PCID2 PCID2 4.40E−04 −10.60 6.02E−04 −7.93 1.27E−03 4.99 1.01E−02 2.47 chr13.41593364-41593568 > ELF1 ELF1 4.35E−04 <−500 9.67E−04 −11.29 4.35E−04 >500 2.23E−03 5.56 chr14.100743755-100744113 > YY1 YY1 4.40E−03 −3.15 1.05E−02 −2.47 2.73E−04 26.26 3.87E−04 13.52 chr14.105236090-105236707 > AKT1 AKT1 4.84E−05 −8.22 2.03E−04 −4.18 2.23E−05 18.04 8.26E−05 6.02 chr14.20872770-20872931 > TEP1 TEP1 1.47E−03 −2.28 8.24E−05 −4.38 3.09E−04 3.06 1.40E−02 1.67 chr14.50246313-50246524 > KLHDC2 KLHDC2 3.77E−02 −1.71 4.58E−04 −5.34 6.75E−03 2.34 1.83E−03 3.20 chr14.52957557-52957723 > TXNDC16 1.34E−04 −4.79 3.06E−03 −2.21 3.24E−04 3.59 7.61E−04 2.90 TXNDC16 chr14.76107075-76107403 > FLVCR2 and 1.92E−03 −2.58 6.71E−05 −9.03 1.22E−01 1.36 6.13E−04 3.38 FLVCR2andTTLL5andC14orf179 TTLL5 and C14orf179 chr14.88431849-88431973 > GALC GALC 5.67E−04 −3.67 2.77E−03 −2.48 1.18E−03 3.01 1.19E−04 7.15 chr14.88452833-88452946 > GALC GALC 3.97E−04 −3.47 2.38E−02 −1.65 8.56E−05 6.09 1.30E−03 2.63 chr14.96997812-96999040 > PAPOLA PAPOLA 1.96E−03 −2.78 6.03E−04 −3.85 3.36E−04 4.77 8.69E−02 1.46 chr15.30711214-30711348 > rukaru rukaru 3.01E−04 −11.05 9.53E−04 −4.94 2.39E−03 3.45 5.73E−03 2.68 chr15.38619054-38620016 > koyzawbu koyzawbu 2.03E−03 −2.87 5.39E−02 −1.58 2.95E−04 5.53 9.82E−04 3.50 chr15.57545460-57545666 > stoyguby stoyguby 3.39E−05 −5.43 8.44E−04 −2.40 9.44E−05 3.83 3.07E−03 1.98 chr15.59102429-59102587 > FAM63B FAM63B 3.05E−03 −3.01 8.90E−04 −4.60 2.53E−04 10.19 5.47E−04 5.82 chr15.59943710-59944525 > GTF2A2 GTF2A2 2.05E−02 −2.18 4.44E−04 −15.25 9.30E−04 7.02 8.26E−03 2.74 chr15.64017491-64017712 > HERC1 HERC1 3.68E−04 −3.52 1.84E−04 −4.37 1.36E−03 2.59 6.20E−03 1.99 chr15.66811217-66811416 > ZWILCH ZWILCH 1.42E−06 −15.75 4.47E−06 −6.69 1.61E−05 4.16 8.06E−05 2.88 chr15.66811217-66811467 > ZWILCH ZWILCH 1.42E−06 −15.75 4.47E−06 −6.69 1.61E−05 4.16 8.06E−05 2.88 chr15.75165540-75165688 > SCAMP2 SCAMP2 4.19E−04 −4.48 6.10E−03 −2.22 1.95E−03 2.82 5.15E−02 1.57 chr15.80191177-80191467 > ST20 and 7.04E−04 −5.57 2.00E−03 −3.59 2.33E−04 13.85 3.18E−04 9.74 ST20andMTHFS MTHFS chr15.94774950-94775234 > MCTP2 MCTP2 4.31E−04 Not 9.26E−04 −11.80 1.11E−03 9.54 4.31E−04 Not Estimable Esti- mable chr16.18799866-18800440 > ARL6IP1 and 2.45E−04 −6.56 2.34E−03 −2.85 1.10E−02 2.06 8.95E−04 3.74 ARL6IP1andRPS15A RPS15A chr16.22277711-22277845 > EEF2K EEF2K 3.16E−05 −114.30 1.08E−04 −8.32 2.29E−02 1.75 3.03E−05 207.60 chr16.30593851-30595166 > syrar syrar 4.87E−05 <−500 6.03E−04 −4.33 4.87E−05 >500 4.87E−05 >500 chr16.3493611-3493837 > ZNF174 and 3.54E−04 <−500 5.17E−04 −24.09 3.54E−04 >500 3.54E−04 >500 ZNF174andNAT15andCLUAP1 NAT15 and CLUAP1 chr17.18087711-18088067 > jeeroy jeeroy 1.76E−04 −13.21 6.59E−04 −4.99 1.02E−04 43.74 1.19E−04 26.41 chr17.18486655-18486837 > CCDC144B 1.37E−02 −2.53 3.39E−04 <−500 3.82E−04 76.21 1.16E−03 7.53 CCDC144B chr17.27581220-27581513 > CRYBA1 CRYBA1 1.03E−04 −21.86 1.74E−03 −3.27 1.66E−04 11.01 2.63E−04 7.47 chr17.36351796-36351996 > TBC1D3 TBC1D3 3.07E−04 −28.30 5.13E−03 −3.10 4.66E−04 12.72 6.73E−04 8.57 chr17.40280569-40280818 > RAB5C RAB5C 2.04E−01 −1.25 8.87E−05 −4.79 2.28E−02 1.61 4.01E−03 2.03 chr17.57728564-57728677 > CLTC CLTC 3.52E−03 −2.77 3.21E−04 −7.06 8.42E−04 4.33 1.79E−03 3.34 chr17.61473104-61473289 > TANC2 TANC2 3.52E−03 −2.04 7.45E−04 −2.65 4.20E−05 6.30 1.10E−05 20.53 chr17.62745780-62746126 > LOC146880 3.51E−03 −2.39 1.24E−03 −3.00 4.23E−04 4.10 2.41E−04 5.09 LOC146880 chr17.77079383-77079672 > ENGASE ENGASE 3.74E−04 Not 2.87E−03 −4.54 2.80E−02 2.14 5.58E−03 3.43 Estimable chr18.48443613-48443878 > ME2 ME2 1.24E−01 −1.52 1.43E−03 −5.39 4.98E−03 3.20 4.15E−04 17.42 chr18.54318248-54318824 > TXNL1 TXNL1 3.27E−04 −6.40 1.59E−04 −11.19 1.61E−03 3.33 1.10E−04 18.33 chr18.67508480-67516323 > DOK6 DOK6 2.50E−06 −3.44 3.70E−07 −5.86 1.18E−04 2.00 1.02E−06 4.24 chr19.11411543-11411912 > tojaw tojaw 1.12E−03 −5.75 3.37E−04 −19.59 4.08E−04 14.07 2.24E−03 4.10 chr19.13009896-13010199 > SYCE2 SYCE2 5.66E−02 −1.66 1.16E−04 −220.29 3.22E−04 9.45 1.70E−04 23.14 chr19.1877203-1877424 > FAM108A1 FAM108A1 9.46E−06 −12.34 3.12E−05 −5.70 4.87E−06 38.02 5.84E−06 24.14 chr19.1953385-1953505 > C19orf34 C19orf34 4.17E−03 −3.77 1.47E−03 −6.50 3.53E−04 Not 9.95E−04 8.89 Esti- mable chr19.36515246-36515534 > CLIP3 CLIP3 5.36E−02 −1.78 2.47E−04 <−500 2.47E−04 >500 2.48E−04 >500 chr19.44128266-44128394 > CADM4 CADM4 1.35E−01 −1.38 7.22E−04 −3.71 2.08E−02 1.80 2.51E−04 5.61 chr19.44619641-44619995 > ZNF225 ZNF225 1.90E−04 −12.35 3.11E−04 −7.83 1.23E−02 2.14 4.26E−04 6.35 chr19.47646729-47646862 > SAE1 SAE1 3.77E−03 −2.25 4.22E−04 −3.71 1.10E−03 2.88 8.17E−02 1.43 chr19.47646751-47646862 > SAE1 SAE1 3.77E−03 −2.25 4.22E−04 −3.71 1.10E−03 2.88 8.17E−02 1.43 chr19.49314066-49314178 > BCAT2 BCAT2 4.79E−03 −3.77 3.15E−03 −4.55 1.48E−03 7.25 4.22E−04 Not Esti- mable chr19.5208248-5208402 > PTPRS PTPRS 2.10E−03 −4.21 4.27E−04 −13.18 8.85E−04 6.65 5.17E−03 3.05 chr19.52207575-52207733 > NCRNA00085 6.15E−05 −5.27 1.16E−05 −18.46 8.15E−06 41.81 1.56E−05 12.72 NCRNA00085 chr19.54610118-54610266 > NDUFA3 NDUFA3 1.16E−04 −6.91 9.25E−03 −1.98 3.81E−05 21.56 4.72E−04 3.80 chr19.58423428-58423554 > ZNF417 and 2.95E−03 −3.70 3.90E−04 −15.56 2.11E−04 >500 1.83E−02 2.20 ZNF417andZNF814 ZNF814 chr19.58423428-58423557 > ZNF417 and 2.95E−03 −3.70 3.90E−04 −15.56 2.11E−04 Not 1.83E−02 2.20 ZNF417andZNF814 ZNF814 Esti- mable chr19.8441789-8441951 > lyta lyta 5.40E−04 −8.82 3.08E−04 −17.86 1.76E−03 4.33 3.90E−03 3.23 chr19.9720432-9722012 > ZNF562 and 6.18E−04 −29.45 4.65E−04 −469.78 4.39E−03 4.01 5.13E−04 75.31 ZNF562andZNF561 ZNF561 chr2.110584278-110584424 > RGPD5 RGPD5 5.04E−05 −11.19 9.25E−04 −3.01 3.59E−04 3.92 1.20E−02 1.87 chr2.111302237-111302383 > RGPD6 RGPD6 5.04E−05 −11.19 9.25E−04 −3.01 3.59E−04 3.92 1.20E−02 1.87 chr2.113175261-113175491 > RGPD8 RGPD8 7.54E−05 −5.13 3.91E−05 −7.04 7.22E−06 >500 1.04E−05 31.99 chr2.118864235-118864479 > INSIG2 INSIG2 5.60E−02 −1.54 1.23E−04 −7.34 2.27E−03 2.62 9.07E−04 3.27 chr2.172848099-172848599 > HAT1 HAT1 1.42E−04 −4.52 4.48E−05 −7.86 8.43E−05 5.58 1.49E−05 29.53 chr2.17953901-17954051 > GEN1 GEN1 9.89E−05 −25.31 6.70E−05 <−500 6.92E−05 199.20 1.58E−03 3.38 chr2.182339687-182340015 > ITGA4 ITGA4 1.90E−05 −7.51 4.08E−03 −1.92 1.03E−04 3.82 1.08E−05 11.34 chr2.198175302-198175503 > ANKRD44 7.11E−04 −5.58 3.26E−04 −9.66 1.03E−02 2.31 2.81E−02 1.89 ANKRD44 chr2.208446079-208446884 > FAM119A 3.71E−05 −9.30 3.05E−04 −3.59 4.39E−03 2.08 5.29E−05 7.28 FAM119A chr2.231663444-231663879 > CAB39 CAB39 6.76E−03 −2.27 1.48E−03 −3.25 3.64E−02 1.69 3.63E−04 5.44 chr2.234112772-234113219 > INPP5D INPP5D 1.03E−03 −3.44 4.25E−04 −4.68 1.22E−04 9.78 2.17E−03 2.82 chr2.242282407-242282508 > SEPT2 SEPT2 4.07E−03 −2.55 1.80E−03 −3.12 1.84E−04 8.63 9.02E−04 3.85 chr2.243168539-243168819 > samemo samemo 4.94E−03 −2.98 1.72E−02 −2.18 2.23E−04 37.87 5.29E−04 8.73 chr2.73957016-73957156 > TPRKB TPRKB 2.11E−05 −8.51 8.41E−06 −23.94 1.24E−05 13.51 6.75E−06 43.24 chr2.88336462-88336570 > KRCC1 KRCC1 1.75E−03 −3.55 5.15E−03 −2.62 2.74E−02 1.86 1.75E−04 15.65 chr20.18449588-18449705 > POLR3F POLR3F 4.95E−05 −10.82 1.16E−03 −2.83 2.93E−04 4.13 1.75E−05 Not Esti- mable chr20.23401942-23402097 > NAPB NAPB 6.00E−05 <−500 4.50E−04 −5.29 5.97E−05 >500 1.09E−04 17.28 chr20.30720816-30720929 > TM9SF4 TM9SF4 4.31E−04 −2.58 7.10E−02 −1.36 1.55E−03 2.11 8.38E−03 1.71 chr20.34487292-34487561 > PHF20 PHF20 1.17E−03 −5.87 7.20E−04 −8.27 4.74E−04 12.86 2.59E−03 3.97 chr20.416929-419485 > TBC1D20 TBC1D20 1.36E−03 −3.68 3.76E−04 −6.52 7.71E−04 4.55 7.72E−03 2.33 chr20.43808628-43808775 > rotora rotora 2.81E−04 −11.96 1.75E−03 −3.84 4.47E−04 7.75 3.40E−03 3.09 chr21.40619627-40619758 > BRWD1 BRWD1 7.54E−05 −4.31 7.25E−06 −21.38 1.26E−05 10.81 3.76E−05 5.59 chr21.47608408-47608855 > klorley klorley 1.80E−02 −2.14 1.56E−03 −4.41 4.26E−04 10.24 6.69E−03 2.71 chr22.20093700-20093800 > DGCR8 DGCR8 6.95E−03 −2.58 8.09E−04 −5.52 2.17E−04 19.30 2.11E−03 3.65 chr22.31733654-31734031 > sneypoy sneypoy 5.37E−02 −1.82 3.99E−04 −39.22 1.49E−03 6.03 1.08E−02 2.67 chr22.41175013-41175129 > SLC25A17 7.16E−04 −7.40 3.66E−04 −14.98 6.05E−03 2.87 9.34E−02 1.58 SLC25A17 chr22.45254869-45255776 > PRR5- PRR5- 1.71E−02 −2.04 9.61E−05 <−500 3.03E−04 8.85 1.52E−03 3.77 ARHGAP8 ARHGAP8 chr22.50320903-50321181 > CRELD2 CRELD2 1.98E−03 −4.87 3.50E−02 −1.97 5.27E−04 14.94 4.59E−04 19.20 chr22.51221467-51221714 > RABL2B RABL2B 4.84E−06 <−500 9.09E−06 −18.75 5.55E−06 85.86 2.67E−05 7.08 chr3.122283274-122283460 > DTX3L DTX3L 3.86E−03 −2.45 8.96E−04 −3.51 1.54E−01 1.35 4.78E−04 4.34 chr3.137963865-137964523 > vusmyby vusmyby 4.47E−04 −6.75 1.85E−02 −2.01 7.96E−04 4.93 2.47E−04 10.96 chr3.137963930-137964523 > ARMC8 ARMC8 4.47E−04 −6.75 1.85E−02 −2.01 7.96E−04 4.93 2.47E−04 10.96 chr3.137963930-137964524 > ARMC8 ARMC8 4.47E−04 −6.75 1.85E−02 −2.01 7.96E−04 4.93 2.47E−04 10.96 chr3.150280329-150280447 > EIF2A EIF2A 1.05E−02 −1.55 4.23E−05 −3.25 1.90E−04 2.48 1.23E−03 1.93 chr3.15778540-15778740 > ANKRD28 ANKRD28 1.71E−04 −3.90 1.21E−05 −23.79 1.60E−03 2.36 2.11E−05 11.26 chr3.167452594-167452717 > PDCD10 PDCD10 4.97E−03 −3.83 4.68E−04 Not 2.62E−03 5.24 1.60E−03 7.32 Estimable chr3.20019802-20020396 > RAB5A RAB5A 4.94E−02 −1.54 3.15E−04 −4.25 8.07E−04 3.20 1.83E−03 2.64 chr3.23929058-23929280 > UBE2E1 UBE2E1 1.32E−03 −3.40 3.40E−04 −5.78 6.07E−02 1.57 2.24E−04 7.41 chr3.25637911-25639423 > RARB RARB 6.84E−03 −2.86 4.19E−02 −1.86 4.93E−04 12.19 2.09E−03 4.35 chr3.39162488-39162680 > TTC21A TTC21A 2.31E−02 −1.64 3.37E−04 −3.48 5.93E−05 6.73 3.03E−05 10.81 chr3.52385978-52386119 > DNAH1 DNAH1 2.86E−05 −25.66 1.71E−04 −5.17 1.52E−02 1.80 3.60E−04 3.92 chr3.52561845-52561947 > NT5DC2 NT5DC2 5.07E−05 Not 5.07E−05 <−500 6.23E−05 50.64 5.07E−05 Not Estimable Esti- mable chr3.69028819-69028938 > C3orf64 C3orf64 4.34E−04 −276.88 1.44E−03 −7.40 6.00E−04 25.32 9.40E−04 11.26 chr3.81552424-81552865 > chordybo chordybo 2.18E−04 −6.44 4.03E−05 Not 4.30E−04 4.65 7.72E−03 2.16 Estimable chr4.122723829-122723948 > EXOSC9 EXOSC9 1.45E−03 −2.35 3.00E−04 −3.21 1.36E−02 1.70 9.05E−05 4.55 chr4.122723829-122723983 > EXOSC9 EXOSC9 1.45E−03 −2.35 3.00E−04 −3.21 1.36E−02 1.70 9.05E−05 4.55 chr4.157731989-157732169 > PDGFC PDGFC 7.75E−04 −2.40 6.25E−03 −1.79 4.00E−05 4.91 9.27E−05 3.76 chr4.175223190-175223337 > KIAA1712 3.59E−04 −10.22 9.07E−02 −1.55 6.69E−03 2.62 1.66E−03 4.04 KIAA1712 chr4.40800804-40800921 > NSUN7 NSUN7 6.85E−02 −1.65 4.03E−04 −10.82 2.93E−04 16.64 1.48E−03 4.51 chr4.76874494-76874938 > sporsmorby sporsmorby 8.09E−03 −2.96 4.72E−04 −28.20 2.56E−02 2.16 2.57E−01 1.34 chr5.134343647-134343829 > PCBD2 and 1.80E−02 −2.37 6.68E−03 −3.17 3.53E−04 Not 5.92E−04 17.76 PCBD2andCATSPER3 CATSPER3 Esti- mable chr5.139929370-139930496 > APBB3 and 2.46E−01 −1.21 2.97E−04 −3.06 1.24E−02 1.69 1.95E−03 2.17 APBB3andSRA1 SRA1 chr5.140895496-140896575 > DIAPH1 DIAPH1 2.42E−03 −3.84 3.56E−04 −14.80 2.77E−04 23.85 9.58E−04 5.96 chr5.140895875-140896575 > DIAPH1 DIAPH1 5.18E−05 −5.97 9.76E−06 −34.42 1.45E−05 16.01 1.20E−05 21.48 chr5.14381239-14381361 > TRIO TRIO 7.18E−04 −3.91 1.44E−02 −1.95 2.22E−04 6.59 1.32E−03 3.25 chr5.145493406-145493874 > LARS LARS 4.03E−04 −11.34 3.32E−03 −3.36 8.40E−04 6.17 5.02E−04 9.06 chr5.35053745-35054334 > fugey fugey 4.00E−04 −9.01 8.14E−04 −5.54 3.29E−04 10.88 1.32E−04 Not Esti- mable chr5.39274505-39274630 > FYB FYB 1.63E−02 −2.33 3.89E−04 −24.35 1.29E−03 6.00 4.56E−02 1.85 chr5.70531277-70532281 > goychyby goychyby 1.10E−02 −2.03 2.29E−04 −6.29 6.59E−04 3.97 2.19E−03 2.81 chr5.77656415-77656552 > SCAMP1 SCAMP1 1.07E−03 −4.46 2.97E−04 −9.88 4.46E−04 7.11 3.67E−02 1.79 chr6.109248281-109249436 > ARMC2 ARMC2 2.72E−03 −2.24 1.30E−02 −1.77 2.08E−04 4.04 8.43E−02 1.40 chr6.122792844-122793050 > SERINC1 1.45E−02 −2.14 5.74E−03 −2.63 2.50E−03 3.31 3.03E−04 9.93 SERINC1 chr6.144289727-144290115 > PLAGL1 and 1.74E−01 −1.44 4.00E−04 −32.52 4.43E−04 23.92 4.81E−03 3.42 PLAGL1andHYMAI HYMAI chr6.153291654-153292549 > FBXO5 FBXO5 3.31E−04 −3.25 1.32E−03 −2.43 4.35E−03 2.01 2.30E−02 1.61 chr6.153291660-153292549 > FBXO5 FBXO5 3.31E−04 −3.25 1.32E−03 −2.43 4.35E−03 2.01 2.30E−02 1.61 chr6.153291674-153292549 > FBXO5 FBXO5 3.31E−04 −3.25 1.32E−03 −2.43 4.35E−03 2.01 2.30E−02 1.61 chr6.158088239-158089557 > fyjaw fyjaw 8.63E−04 −4.25 2.52E−02 −1.85 1.77E−03 3.33 2.99E−04 7.26 chr6.3021094-3022352 > teyvybo teyvybo 3.80E−05 −140.84 4.06E−05 −74.72 9.11E−04 3.45 1.27E−04 8.48 chr6.34360041-34360260 > RPS10 and 5.81E−04 −4.24 8.57E−05 −15.64 7.24E−05 20.73 1.60E−04 8.25 RPS10andNUDT3 NUDT3 chr6.41036580-41036692 > C6orf130 and 3.57E−04 −5.13 1.22E−04 −10.16 7.37E−04 3.87 1.49E−03 3.13 C6orf130andUNC5CL UNC5CL chr6.41751200-41751976 > PRICKLE4 and 4.62E−03 −2.80 2.51E−04 −12.58 4.03E−04 7.96 9.63E−04 4.78 PRICKLE4andTOMM6 TOMM6 chr6.79664949-79665569 > PHIP and 1.35E−03 −2.92 2.55E−05 Not 1.30E−04 6.84 5.14E−05 15.62 PHIPandTRNAF13P TRNAF13P Estimable chr7.149598-152547 > kehera kehera 1.33E−02 −1.71 1.29E−03 −2.42 9.72E−02 1.36 4.40E−04 2.99 chr7.22980878-22987334 > FAM126A FAM126A 5.13E−04 −2.56 4.24E−05 −4.72 8.77E−03 1.71 1.84E−03 2.09 chr7.2635311-2636062 > dochuby dochuby 3.67E−04 −4.19 1.69E−04 −5.80 4.01E−03 2.30 2.63E−02 1.70 chr7.29549802-29552165 > klerky klerky 1.88E−04 −6.48 3.73E−03 −2.44 2.29E−02 1.77 8.77E−02 1.46 chr7.45083306-45083697 > CCM2 CCM2 2.52E−02 −1.90 8.39E−04 −4.83 1.36E−03 3.96 3.71E−04 7.72 chr7.5938415-5938550 > CCZ1 CCZ1 5.04E−07 −252.68 2.41E−06 −8.08 7.48E−06 4.89 1.37E−06 12.27 chr7.74166365-74166897 > GTF2I GTF2I 2.27E−03 −3.76 5.26E−04 −8.20 7.50E−04 6.36 2.45E−04 22.31 chr7.76870183-76870364 > CCDC146 CCDC146 1.69E−05 −12.37 4.46E−05 −6.24 4.43E−04 2.97 6.52E−06 Not Esti- mable chr8.104455023-104455428 > DCAF13 DCAF13 4.47E−02 −1.81 1.12E−02 −2.44 5.04E−03 3.04 4.85E−04 10.67 chr8.133984843-133984986 > TG TG 3.27E−02 −1.99 2.69E−04 <−500 2.69E−04 Not 2.69E−04 >500 Esti- mable chr8.24256387-24256553 > ADAMDEC1 1.89E−02 −2.37 1.55E−03 −6.56 3.81E−04 Not 5.79E−02 1.82 ADAMDEC1 Esti- mable chr8.30948350-30948458 > WRN WRN 9.84E−05 −8.13 4.33E−05 −19.99 6.54E−04 3.52 1.58E−04 6.10 chr8.62438536-62438671 > ASPH ASPH 1.08E−03 −5.20 5.24E−03 −2.88 2.06E−02 2.07 3.63E−04 11.88 chr8.74858684-74859055 > TCEB1 TCEB1 2.36E−04 −11.51 1.83E−04 −16.10 3.38E−04 8.24 1.05E−03 4.38 chr9.17135038-17135423 > CNTLN CNTLN 3.03E−02 −1.91 1.90E−03 −3.97 8.64E−04 5.73 4.80E−04 8.60 chr9.33264164-33264493 > CHMP5 CHMP5 1.44E−04 −11.82 8.33E−04 −4.08 1.94E−04 8.91 4.09E−04 5.53 chr9.35737655-35737936 > GBA2 GBA2 6.33E−03 −3.43 4.89E−04 −96.76 1.37E−03 8.06 5.25E−04 55.35 chrX.118985730-118985836 > UPF3B UPF3B 1.13E−04 <−500 1.55E−03 −3.93 3.89E−03 2.93 8.72E−04 4.99 chrX.138864706-138864887 > ATP11C ATP11C 3.68E−03 −3.31 2.76E−04 −23.71 1.59E−02 2.23 9.95E−04 5.80 chrX.149924161-149924396 > MTMR1 MTMR1 1.84E−03 −6.49 4.58E−04 <−500 2.92E−03 4.89 6.99E−03 3.33 chrX.153744234-153744566 > FAM3A FAM3A 1.07E−04 −54.24 3.85E−04 −7.03 2.63E−04 9.43 8.88E−04 4.53 chrX.15862547-15863639 > AP1S2 AP1S2 9.09E−05 −5.62 1.65E−04 −4.42 4.01E−03 2.12 6.08E−02 1.46 chrX.16870674-16871149 > RBBP7 RBBP7 6.02E−03 −2.99 2.65E−03 −3.99 8.60E−04 7.37 3.25E−04 29.04 chrX.2839944-2840065 > ARSD ARSD 1.44E−03 −3.53 4.55E−02 −1.67 3.00E−03 2.86 3.95E−04 6.06 chrX.74282163-74282417 > ABCB7 ABCB7 1.09E−03 −5.81 8.03E−04 −7.10 1.32E−02 2.36 3.38E−04 19.17 chrX.76776266-76776394 > ATRX ATRX 3.40E−06 −5.28 1.40E−04 −2.35 1.89E−03 1.75 6.84E−06 4.23 chrX.77303661-77305892 > ATP7A ATP7A 1.55E−04 −10.33 2.03E−03 −3.04 3.29E−01 1.22 1.05E−03 3.70 CE Stroke vs. Controls vs. Controls vs. Controls vs. Controls ICH LV Lacunar Upregulated in Controls p- p- p- p- Marker ID Gene Symbol value FC value FC value FC value FC chr1.53416427-53416558 > SCP2 SCP2 4.14E−04 −3.65 3.66E−02 1.59 1.42E−03 2.69 6.07E−03 2.06 chr14.19683027-19683434 > DUXAP10 DUXAP10 3.62E−05 −29.94 1.14E−04 7.36 2.52E−05 >500 4.66E−05 17.76 chr17.42982993-42984756 > GFAP GFAP 6.98E−04 −5.06 1.25E−02 2.15 4.86E−03 2.65 2.89E−04 8.76 chr18.28642978-28643439 > DSC2 DSC2 2.44E−02 −1.84 5.93E−03 2.41 1.09E−03 3.79 1.88E−04 9.74 chr18.43417478-43417850 > SIGLEC15 SIGLEC15 3.26E−04 <−500 2.04E−03 5.10 1.43E−02 2.49 4.84E−02 1.87 chr19.39138368-39138547 > ACTN4 ACTN4 1.33E−05 −8.92 1.30E−04 3.51 5.83E−06 22.30 3.57E−05 5.30 chr19.45543176-45543569 > SFRS16 SFRS16 1.43E−04 <−500 4.87E−03 2.87 3.81E−04 9.97 2.38E−04 18.83 chr2.101606718-101606908 > NPAS2 NPAS2 2.57E−04 −6.61 5.03E−04 4.72 7.16E−05 30.24 3.23E−03 2.67 chr2.242611606-242612016 > ATG4B ATG4B 8.42E−05 −8.04 3.53E−05 20.98 1.89E−04 5.17 1.07E−03 2.97 chr20.32880178-32880359 > AHCY AHCY 2.22E−03 −4.21 5.50E−03 3.04 3.66E−04 18.76 1.14E−02 2.48 chr22.36892014-36892255 > FOXRED2 and 2.48E−04 −5.82 1.19E−02 1.99 4.04E−03 2.43 7.88E−02 1.49 FOXRED2andTXN2 TXN2 chr22.41252435-41253036 > ST13 ST13 1.56E−03 −7.62 3.49E−03 4.55 4.81E−04 >500 4.81E−04 >500 chr6.32806430-32806547 > TAP2andHLA- TAP2 and 9.55E−05 <−500 2.92E−03 3.07 2.70E−04 9.81 7.48E−04 5.03 DOB HLA-DOB chr7.101475858-101476865 > snorkar snorkar 2.78E−04 −23.06 2.33E−02 2.05 2.70E−03 3.68 6.83E−03 2.75 chr9.140473077-140473340 > WDR85 WDR85 3.68E−05 −31.77 4.74E−04 3.93 1.31E−04 6.90 6.73E−05 11.64 chr9.95018962-95019082 > IARS IARS 1.52E−05 −7.76 2.30E−04 3.02 7.17E−05 4.05 2.90E−05 5.60 chr9.96866557-96866667 > PTPDC1 PTPDC1 3.10E−07 Not 7.27E−04 1.95 8.40E−07 13.03 3.13E−07 >500 Estimable chrX.48367956-48368344 > PORCN PORCN 4.63E−05 −86.44 4.10E−05 >500 4.91E−05 58.47 7.98E−05 16.02

TABLE 8 Over-represented Pathways and Gene Ontology for the Upregulated Exons Cardioembolic Stroke SIGNIFICANTLY ENRICHED CANONICAL PATHWAYS OF CARDIOEMBOLIC STROKE Ingenuity Canonical B-H Pathways −log(p-value) p-value Ratio Molecules Semaphorin 1.41E00 6.9E−03-7.47E−02 1.89E−02 PLXNB1 Signaling in Neurons GENE ONTOLOGY OF CARDIOEMBOLIC STROKE List Pop Pop Fold Category Term Count % PValue Genes Total Hits Total Enrichment Benjamini FDR Annotation Cluster 1 Enrichment Score: 1.5478345985149118 GOTERM_MF_FAT GO: 0046872~metal ion 9 47.37 0.03 STEAP3, ZNF33A, UPF1, LPP, ZNF417, 14 4140 12983 2.02 0.89 24.97 binding ZNF814, TRPV5, TTN, SLC10A1 GOTERM_MF_FAT GO: 0043169~cation 9 47.37 0.03 STEAP3, ZNF33A, UPF1, LPP, ZNF417, 14 4179 12983 2.00 0.69 26.24 binding ZNF814, TRPV5, TTN, SLC10A1 GOTERM_MF_FAT GO: 0043167~ion binding 9 47.37 0.03 STEAP3, ZNF33A, UPF1, LPP, ZNF417, 14 4241 12983 1.97 0.58 28.33 ZNF814, TRPV5, TTN, SLC10A1 Annotation Cluster 2 Enrichment Score: 1.4272404656779223 GOTERM_CC_FAT GO: 0005887~integral to 4 21.05 0.03 PLXNB1, PTPRN2, TRPV5, SLC10A1 9 1188 12782 4.78 0.75 25.81 plasma membrane GOTERM_CC_FAT GO: 0031226~intrinsic to 4 21.05 0.03 PLXNB1, PTPRN2, TRPV5, SLC10A1 9 1215 12782 4.68 0.53 27.17 plasma membrane GOTERM_CC_FAT GO: 0044459~plasma 5 26.32 0.03 PLXNB1, LPP, PTPRN2, TRPV5, SLC10A1 9 2203 12782 3.22 0.40 27.86 membrane part GOTERM_CC_FAT GO: 0005886~plasma 6 31.58 0.05 STEAP3, PLXNB1, LPP, PTPRN2, TRPV5, 9 3777 12782 2.26 0.46 40.79 membrane SLC10A1 Annotation Cluster 3 Enrichment Score: 1.228190007997564 GOTERM_BP_FAT GO: 0030001~metal ion 3 15.79 0.05 STEAP3, TRPV5, SLC10A1 12 465 13528 7.27 1.00 48.17 transport GOTERM_CC_FAT GO: 0005886~plasma 6 31.58 0.05 STEAP3, PLXNB1, LPP, PTPRN2, TRPV5, 9 3777 12782 2.26 0.46 40.79 membrane SLC10A1 GOTERM_BP_FAT GO: 0006812~cation 3 15.79 0.07 STEAP3, TRPV5, SLC10A1 12 553 13528 6.12 1.00 59.48 transport Large Vessel IS SIGNIFICANTLY ENRICHED CANONICAL PATHWAYS OF LARGE VESSEL ISCHEMIC STROKE Ingenuity −log(B-H Canonical Pathways −log(p-value) p-value) Ratio Molecules Oxidized GTP and 2.44E00 1E00 3.33E−01 NUDT1 dGTP Detoxification UDP-N-acetyl-D- 2.14E00 1E00 1.67E−01 GNPNAT1 glucosamine Biosynthesis II Glycoaminoglycan- 2.08E00 1E00 1.43E−01 B3GAT3 protein Linkage Region Biosynthesis UDP-N-acetyl-D- 1.97E00 1E00 1.11E−01 GNPNAT1 galactosamine Biosynthesis II Thyroid Hormone 1.44E00 7.92E−01   3.23E−02 B3GAT3 Metabolism II (via Conjugation and/or Degradation) Nucleotide Excision 1.38E00 7.92E−01   2.86E−02 ERCC5 Repair Pathway GENE ONTOLOGY OF LARGE VESSEL ISCHEMIC STROKE List Pop Pop Fold Category Term Count % PValue Genes Total Hits Total Enrichment Benjamini FDR Annotation Cluster 1 Enrichment Score: 1.9116473785151364 GOTERM_CC_FAT GO: 0070013~intracellular 8 26.67 0.01 PDK1, ERCC5, PNMA3, CENPF, PCSK6, 20 1779 12782 2.87 0.64 11.29 organelle lumen DIMT1L, DNAJA3, CBX5 GOTERM_CC_FAT GO: 0043233~organelle 8 26.67 0.01 PDK1, ERCC5, PNMA3, CENPF, PCSK6, 20 1820 12782 2.81 0.43 12.68 lumen DIMT1L, DNAJA3, CBX5 GOTERM_CC_FAT GO: 0031974~membrane- 8 26.67 0.01 PDK1, ERCC5, PNMA3, CENPF, PCSK6, 20 1856 12782 2.75 0.34 13.98 enclosed lumen DIMT1L, DNAJA3, CBX5 Annotation Cluster 2 Enrichment Score: 1.6656724740255078 GOTERM_BP_FAT GO: 0043066~negative 4 13.33 0.01 ERCC5, RIPK2, PCSK6, DNAJA3 20 354 13528 7.64 1.00 16.49 regulation of apoptosis GOTERM_BP_FAT GO: 0043069~negative 4 13.33 0.01 ERCC5, RIPK2, PCSK6, DNAJA3 20 359 13528 7.54 0.95 17.07 regulation of programmed cell death GOTERM_BP_FAT GO: 0060548~negative 4 13.33 0.01 ERCC5, RIPK2, PCSK6, DNAJA3 20 360 13528 7.52 0.87 17.19 regulation of cell death GOTERM_BP_FAT GO: 0042981~regulation of 4 13.33 0.10 ERCC5, RIPK2, PCSK6, DNAJA3 20 804 13528 3.37 0.96 77.51 apoptosis Annotation Cluster 3 Enrichment Score: 1.3439751095199926 GOTERM_BP_FAT GO: 0016481~negative 4 13.33 0.03 LMCD1, CENPF, NSD1, CBX5 20 459 13528 5.89 0.94 30.30 regulation of transcription GOTERM_MF_FAT GO: 0003682~chromatin 3 10.00 0.03 CENPF, NSD1, CBX5 24 150 12983 10.82 0.98 28.76 binding GOTERM_BP_FAT GO: 0010629~negative 4 13.33 0.03 LMCD1, CENPF, NSD1, CBX5 20 504 13528 5.37 0.95 36.94 regulation of gene expression GOTERM_BP_FAT GO: 0045934~negative 4 13.33 0.03 LMCD1, CENPF, NSD1, CBX5 20 512 13528 5.28 0.89 38.15 regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GOTERM_BP_FAT GO: 0051172~negative 4 13.33 0.03 LMCD1, CENPF, NSD1, CBX5 20 519 13528 5.21 0.86 39.20 regulation of nitrogen compound metabolic process GOTERM_BP_FAT GO: 0010558~negative 4 13.33 0.04 LMCD1, CENPF, NSD1, CBX5 20 547 13528 4.95 0.87 43.44 regulation of macromolecule biosynthetic process GOTERM_BP_FAT GO: 0031327~negative 4 13.33 0.04 LMCD1, CENPF, NSD1, CBX5 20 561 13528 4.82 0.86 45.56 regulation of cellular biosynthetic process GOTERM_BP_FAT GO: 0009890~negative 4 13.33 0.04 LMCD1, CENPF, NSD1, CBX5 20 573 13528 4.72 0.84 47.38 regulation of biosynthetic process GOTERM_MF_FAT GO: 0008134~transcription 4 13.33 0.06 LMCD1, CENPF, NSD1, DNAJA3 24 513 12983 4.22 0.98 51.71 factor binding GOTERM_BP_FAT GO: 0010605~negative 4 13.33 0.08 LMCD1, CENPF, NSD1, CBX5 20 734 13528 3.69 0.96 69.72 regulation of macromolecule metabolic process GOTERM_BP_FAT GO: 0045892~negative 3 10.00 0.09 LMCD1, NSD1, CBX5 20 356 13528 5.70 0.96 72.98 regulation of transcription, DNA-dependent GOTERM_BP_FAT GO: 0051253~negative 3 10.00 0.09 LMCD1, NSD1, CBX5 20 362 13528 5.61 0.95 74.03 regulation of RNA metabolic process Lacunar IS Ingenuity −log(B-H Canonical Pathways −log(p-value) p-value) Ratio Molecules SIGNIFICANTLY ENRICHED CANONICAL PATHWAYS OF LACUNAR ISCHEMIC STROKE Eumelanin 2.34E00 7.03E−01 2.5E−01 DDT Biosynthesis G Protein Signaling 1.43E00 6.15E−01 3.03E−02 GNG3 Mediated by Tubby GENE ONTOLOGY OF LACUNAR ISCHEMIC STROKE Not Available with 0.1 Ease Intracerebral hemorrhage (ICH) SIGNIFICANTLY ENRICHED CANONICAL PATHWAYS OF HEM Regulation of elF4 3.54E00 1.14E00  4.79E−02 SHC1, AKT1, RPS10, ITGA5, RPS15A, EIF2A, ITGA4 and p70S6K Signaling PTEN Signaling 3.24E00 1.14E00  5.08E−02 MAST2, SHC1, AKT1, ITGA5, INPP5D, ITGA4 Actin Cytoskeleton 2.53E00 8.12E−01 3.23E−02 SHC1, DIAPH1, ITGA5, TRIO, SLC9A1, PDGFC, ITGA4 Signaling IL-3 Signaling 2.47E00 8.12E−01 5.63E−02 SHC1, AKT1, PPP3CB, INPP5D Caveolar-mediated 2.45E00 8.12E−01 5.56E−02 RAB5A, RAB5C, ITGA5, ITGA4 Endocytosis Signaling Ephrin Receptor 2.38E00 8.12E−01 3.45E−02 SHC1, AKT1, ITGA5, GNG5, PDGFC, ITGA4 Signaling PI3K/AKT Signaling 2.36E00 8.12E−01 4.07E−02 SHC1, AKT1, ITGA5, INPP5D, ITGA4 FcγRIIB Signaling in 2.27E00 8.12E−01 7.32E−02 SHC1, AKT1, INPP5D B Lymphocytes Clathrin-mediated 2.25E00 8.12E−01 3.24E−02 RAB5A, RAB5C, PPP3CB, CLTC, ITGA5, PDGFC Endocytosis Signaling DNA Double-Strand 2.2E00 8.08E−01 1.43E−01 GEN1, ATRX Break Repair by Homologous Recombination Neuregulin 2.14E00 8.08E−01 4.55E−02 SHC1, AKT1, ITGA5, ITGA4 Signaling PAK Signaling 2.12E00 8.08E−01 4.49E−02 SHC1, ITGA5, PDGFC, ITGA4 Telomerase 1.96E00 6.84E−01 4.04E−02 SHC1, AKT1, TEP1, ELF1 Signaling HGF Signaling 1.88E00 6.48E−01 3.81E−02 AKT1, ITGA5, ELF1, ITGA4 iCOS-iCOSL 1.83E00 6.48E−01  3.7E−02 SHC1, AKT1, PPP3CB, INPP5D Signaling in T Helper Cells Natural Killer Cell 1.81E00 6.48E−01 3.64E−02 SHC1, AKT1, KLRC4-KLRK1/KLRK1, INPP5D Signaling GM-CSF Signaling 1.78E00 6.48E−01 4.84E−02 SHC1, AKT1, PPP3CB 4-hydroxyproline 1.76E00 6.48E−01   5E−01 HOGA1 Degradation I Anandamide 1.76E00 6.48E−01   5E−01 FAAH Degradation Macropinocytosis 1.67E00  5.8E−01 4.41E−02 RAB5A, ITGA5, PDGFC Signaling ElF2 Signaling 1.64E00  5.8E−01  2.7E−02 SHC1, AKT1, RPS10, RPS15A, EIF2A mTOR Signaling 1.61E00  5.8E−01 2.66E−02 AKT1, RPS10, RPS15A, PDGFC, ARHGAP8/PRR5-ARHGAP8 NF-κB Activation by 1.59E00 5.8E−01 4.11E−02 AKT1, ITGA5, ITGA4 Viruses Tyrosine 1.59E00 5.8E−01 3.33E−01 PCBD2 Biosynthesis IV FLT3 Signaling in 1.57E00 5.8E−01 4.05E−02 SHC1, AKT1, INPP5D Hematopoietic Progenitor Cells IL-4 Signaling 1.55E00 5.69E−01 3.95E−02 SHC1, AKT1, INPP5D PDGF Signaling 1.53E00 5.69E−01  3.9E−02 SHC1, PDGFC, INPP5D Reelin Signaling in  1.5E00 5.57E−01  3.8E−02 AKT1, ITGA5, ITGA4 Neurons Phenylalanine 1.46E00 5.35E−01  2.5E−01 PCBD2 Degradation I (Aerobic) FAK Signaling  1.4E00   5E−01 3.45E−02 AKT1, ITGA5, ITGA4 CTLA4 Signaling in 1.38E00   5E−01 3.41E−02 AKT1, AP1S2, CLTC Cytotoxic T Lymphocytes G Beta Gamma 1.38E00   5E−01 3.41E−02 SHC1, AKT1, GNG5 Signaling Virus Entry via 1.37E00   5E−01 3.37E−02 CLTC, ITGA5, ITGA4 Endocytic Pathways VEGF Signaling 1.35E00   5E−01  3.3E−02 SHC1, AKT1, PDGFC Fcγ Receptor- 1.32E00   5E−01 3.23E−02 AKT1, FYB, INPP5D mediated Phagocytosis in Macrophages and Monocytes PPAR Signaling 1.31E00   5E−01 3.19E−02 SHC1, SRA1, PDGFC Tec Kinase 1.31E00   5E−01 2.53E−02 GTF2I, ITGA5, GNG5, ITGA4 Signaling Glioma Signaling  1.3E00   5E−01 3.16E−02 SHC1, AKT1, PDGFC Huntington's  1.3E00   5E−01 2.17E−02 SHC1, AKT1, CLTC, GNG5, NAPB Disease Signaling GENE ONTOLOGY OF HEM List Pop Pop Fold Category Term Count % PValue Genes Total Hits Total Enrichment Benjamini FDR Annotation Cluster 1 Enrichment Score: 2.0008035747785273 GOTERM_BP_FAT GO: 0015031~protein 19 10.05291005 6.74E−04 RGPD6, SCAMP1, ARL6IP1, FYB, RGPD5, 138 762 13528 2.44 0.57 1.09 transport RGPD8, SCAMP2, RAB5C, CHMP5, NAPB, CLTC, AKT1, SFT2D2, AP1S2, TOMM6, ATG4C, LYST, FXC1, TOMM40L, RAB5A, PPP3CB GOTERM_BP_FAT GO: 0045184~establishment 19 10.05291005 7.50E−04 RGPD6, SCAMP1, ARL6IP1, FYB, RGPD5, 138 769 13528 2.42 0.37 1.21 of protein localization RGPD8, SCAMP2, RAB5C, CHMP5, NAPB, CLTC, AKT1, SFT2D2, AP1S2, TOMM6, ATG4C, LYST, FXC1 TOMM40L, RAB5A, PPP3CB GOTERM_BP_FAT GO: 0008104~protein 19 10.05291005 3.43E−03 RGPD6, SCAMP1, ARL6IP1, FYB, RGPD5, 138 882 13528 2.11 0.76 5.43 localization RGPD8, SCAMP2, RAB5C, CHMP5, NAPB, CLTC, AKT1, SFT2D2, AP1S2, TOMM6, ATG4C, LYST, FXC1, TOMM40L, RAB5A, PPP3CB GOTERM_BP_FAT GO: 0046907~intracellular 15 7.936507937 6.75E−03 RGPD6, ARL6IP1, FYB, SCAMP1, RGPD5, 138 657 13528 2.24 0.88 10.42 transport RGPD8, SCAMP2, KIF5B, CHMP5, NAPB, CLTC, AKT1, AP1S2, ATG4C, LYST, FXC1, PPP3CB GOTERM_BP_FAT GO: 0006886~intracellular 9 4.761904762 3.64E−02 FYB, ARL6IP1, AKT1, AP1S2, ATG4C, FXC1, 138 374 13528 2.36 1.00 45.30 protein transport PPP3CB, NAPB, CLTC GOTERM_BP_FAT GO: 0034613~cellular 9 4.761904762 5.75E−02 FYB, ARL6IP1, AKT1, AP1S2, ATG4C, FXC1, 138 411 13528 2.15 1.00 61.82 protein localization PPP3CB, NAPB, CLTC GOTERM_BP_FAT GO: 0070727~cellular 9 4.761904762 5.95E−02 FYB, ARL6IP1, AKT1, AP1S2, ATG4C, FXC1, 138 414 13528 2.13 1.00 63.10 macromolecule PPP3CB, NAPB, CLTC localization GOTERM_BP_FAT GO: 0006605~protein 6 3.174603175 6.75E−02 FYB, ARL6IP1, AKT1, ATG4C, FXC1, PPP3CB 138 215 13528 2.74 0.99 67.90 targeting Annotation Cluster 2 Enrichment Score: 1.946654262059368 GOTERM_CC_FAT GO: 0015630~microtubule 16 8.465608466 3.54E−04 SDCCAG8, SEPT2, KIF5B, TTLL5, DNHD1, 128 549 12782 2.91 0.09 0.46 cytoskeleton CHEK1, DNAH1, WRN, AKT1, PBXIP1, CEP350, ATG4C, NAV1, LYST, FBXO5, CNTLN GOTERM_CC_FAT GO: 0005856~cytoskeleton 23 12.16931217 1.70E−02 FYB, CTTNBP2NL, SDCCAG8, SEPT2, KIF5B, 128 1381 12782 1.66 0.58 20.05 DIAPH1, UBR4, DNHD1, TTLL5, DNAH1, CHEK1, WRN, ZNF174, AKT1, MAST2, PBXIP1, NAV1, CEP350, ATG4C, LYST, FAAH, FBXO5, CNTLN GOTERM_CC_FAT GO: 0043232~intracellular 37 19.57671958 1.85E−02 CTTNBP2NL, SDCCAG8, SEPT2, HMGN2, 128 2596 12782 1.42 0.54 21.53 non-membrane-bounded DIAPH1, RPS15A, TTLL5, DNAH1, CHEK1, organelle ZNF174, AKT1, DCAF13, PBXIP1, DGCR8, FBXO5, CNTLN, ZWILCH, FYB, EXOSC9, KIF5B, UBR4, SYCE2, DNHD1, WRN, EXOSC1, ATRX, PAPOLA, MAST2, NAV1, APITD1, CEP350, ATG4C, LYST, FAAH, TEP1, RPS10, CORT, TBX19 GOTERM_CC_FAT GO: 0043228~non- 37 19.57671958 1.85E−02 CTTNBP2NL, SDCCAG8, SEPT2, HMGN2, 128 2596 12782 1.42 0.54 21.53 membrane-bounded DIAPH1, RPS15A, TTLL5, DNAH1, CHEK1, organelle ZNF174, AKT1, DCAF13, PBXIP1, DGCR8, FBXO5, CNTLN, ZWILCH, FYB, EXOSC9, KIF5B, UBR4, SYCE2, DNHD1, WRN, EXOSC1, ATRX, PAPOLA, MAST2, NAV1, APITD1, CEP350, ATG4C, LYST, FAAH, TEP1, RPS10, CORT, TBX19 GOTERM_CC_FAT GO: 0044430~cytoskeletal 15 7.936507937 9.00E−02 SDCCAG8, SEPT2, KIF5B, TTLL5, DNHD1, 128 952 12782 1.57 0.68 70.68 part CHEK1, DNAH1, WRN, AKT1, PBXIP1, CEP350, ATG4C, NAV1, FBXO5, CNTLN Annotation Cluster 3 Enrichment Score: 1.4567585294932377 GOTERM_CC_FAT GO: 0030136~clathrin- 6 3.174603175 0.01 SCAMP1, ATP7A, AP1S2, PI4K2A, RAB5A, 128 132 12782 4.54 0.58 12.44 coated vesicle CLTC GOTERM_CC_FAT GO: 0030665~clathrin 4 2.116402116 0.02 SCAMP1, AP1S2, PI4K2A, CLTC 128 53 12782 7.54 0.63 18.55 coated vesicle membrane GOTERM_BP_FAT GO: 0006892~post-Golgi 4 2.116402116 0.02 SCAMP1, AP1S2, SCAMP2, CLTC 138 58 13528 6.76 0.99 29.07 vesicle-mediated transport GOTERM_CC_FAT GO: 0030135~coated 6 3.174603175 0.02 SCAMP1, ATP7A, AP1S2, PI4K2A, RAB5A, 128 159 12782 3.77 0.54 24.29 vesicle CLTC GOTERM_CC_FAT GO: 0030140~trans-Golgi 3 1.587301587 0.02 ATP7A, AP1S2, CLTC 128 24 12782 12.48 0.49 26.56 network transport vesicle GOTERM_CC_FAT GO: 0030133~transport 4 2.116402116 0.03 ATP7A, AP1S2, PI4K2A, CLTC 128 66 12782 6.05 0.51 30.76 vesicle GOTERM_CC_FAT GO: 0030662~coated 4 2.116402116 0.04 SCAMP1, AP1S2, PI4K2A, CLTC 128 73 12782 5.47 0.54 37.96 vesicle membrane GOTERM_CC_FAT GO: 0005768~endosome 8 4.232804233 0.04 SCAMP1, ATP7A, SCAMP2, RAB5C, CHMP5, 128 315 12782 2.54 0.53 39.32 PI4K2A, RAB5A, CYBASC3 GOTERM_CC_FAT GO: 0030659~cytoplasmic 5 2.645502646 0.05 SCAMP1, AP1S2, PI4K2A, RAB5A, CLTC 128 139 12782 3.59 0.60 48.53 vesicle membrane GOTERM_CC_FAT GO: 0012506~vesicle 5 2.645502646 0.06 SCAMP1, AP1S2, PI4K2A, RAB5A, CLTC 128 151 12782 3.31 0.65 57.50 membrane GOTERM_CC_FAT GO: 0044431~Golgi 7 3.703703704 0.07 SCAMP1, ATP7A, AP1S2, SCAMP2, PDGFC, 128 294 12782 2.38 0.68 62.65 apparatus part CLIP3, CLTC GOTERM_CC_FAT GO: 0012505~endomembrane 13 6.878306878 0.09 ARL6IP1, SCAMP1, RGPD6, RGPD5, RGPD8, 128 782 12782 1.66 0.69 69.95 system SCAMP2, CLTC, AP1S2, STT3A, INSIG2, SERINC1, PI4K2A, RAB5A, PDGFC, ASPH GOTERM_CC_FAT GO: 0005798~Golgi- 3 1.587301587 0.09 ATP7A, AP1S2, CLTC 128 51 12782 5.87 0.67 71.19 associated vesicle Annotation Cluster 4 Enrichment Score: 1.2483614903873126 GOTERM_BP_FAT GO: 0006665~sphingolipid 4 2.116402116 0.04 GBA2, SERINC1, LASS2, GALC 138 75 13528 5.23 1.00 48.90 metabolic process GOTERM_BP_FAT GO: 0006643~membrane 4 2.116402116 0.05 GBA2, SERINC1, LASS2, GALC 138 81 13528 4.84 1.00 55.78 lipid metabolic process GOTERM_BP_FAT GO: 0006672~ceramide 3 1.587301587 0.07 GBA2, LASS2, GALC 138 42 13528 7.00 1.00 67.83 metabolic process GOTERM_BP_FAT GO: 0046519~sphingoid 3 1.587301587 0.08 GBA2, LASS2, GALC 138 45 13528 6.54 1.00 72.33 metabolic process Annotation Cluster 5 Enrichment Score: 1.1612816039563372 GOTERM_CC_FAT GO: 0042470~melanosome 4 2.116402116 0.06 RAB5C, RAB5A, CLTC, PRDX1 128 89 12782 4.49 0.64 54.53 GOTERM_CC_FAT GO: 0048770~pigment 4 2.116402116 0.06 RAB5C, RAB5A, CLTC, PRDX1 128 89 12782 4.49 0.64 54.53 granule GOTERM_CC_FAT GO: 0009898~internal side 7 3.703703704 0.10 AP1S2, MTMR1, MAST2, RAB5C, RAB5A, 128 316 12782 2.21 0.67 72.75 of plasma membrane CLTC, GNG5 Controls SIGNIFICANTLY ENRICHED CANONICAL PATHWAYS OF CONTROLS Ingenuity −log(B-H Canonical Pathways −log(p-value) p-value) Ratio Molecules Antigen 3.35E00 1.71E00 5.41E−02 HLA-DOB, TAP2 Presentation Pathway Bile Acid 1.96E00 8.31E−01 7.69E−02 SCP2 Biosynthesis, Neutral Pathway Methionine 1.87E00 8.31E−01 6.25E−02 AHCY Degradation I (to Homocysteine) Cysteine 1.82E00 8.31E−01 5.56E−02 AHCY Biosynthesis III (mammalia) Superpathway of 1.58E00 8.31E−01 3.23E−02 AHCY Methionine Degradation B Cell Development 1.54E00 8.31E−01 2.94E−02 HLA-DOB tRNA Charging 1.48E00 8.31E−01 2.56E−02 IARS Graft-versus-Host  1.4E00 8.31E−01 2.08E−02 HLA-DOB Disease Signaling Autoimmune 1.39E00 8.31E−01 2.04E−02 HLA-DOB Thyroid Disease Signaling Primary 1.36E00 8.31E−01 1.92E−02 TAP2 Immunodeficiency Signaling Nur77 Signaling in 1.32E00 8.31E−01 1.75E−02 HLA-DOB T Lymphocytes Regulation of 1.32E00 8.31E−01 1.75E−02 ACTN4 Cellular Mechanics by Calpain Protease SIGNIFICANTLY ENRICHED CANONICAL PATHWAYS OF CONTROLS Annotation Cluster 1 Enrichment Score: 1.556431804209894 List Pop Pop Fold Category Term Count % PValue Genes Total Hits Total Enrichment Benjamini FDR GOTERM_CC_FAT GO: 0044432~endoplasmic 4 21.05263158 0.00 TAP2, FOXRED2, HLA-DOB, PORCN 14  347 12782 10.52  0.30  4.79 reticulum part GOTERM_MF_FAT GO: 0001882~nucleoside 5 26.31578947 0.07 IARS, ACTN4, TAP2, FOXRED2, HLA-DOB 14 1612 12983 2.88 1.00 52.67 binding GOTERM_CC_FAT GO: 0005783~endoplasmic 4 21.05263158 0.07 TAP2, FOXRED2, HLA-DOB, PORCN 14 960 12782 3.80 0.94 52.80 reticulum

Discussion

Although DAS is implicated in many human diseases, this is the first study to report DAS for ICH, IS and controls, and is the first to show that DAS is different for different causes of IS. Identification of specific DAS for different stroke etiologies suggests the immune response varies for each condition. This will likely be important for understanding pathogenesis of each stroke cause and biomarker development.

This study identified several pathways, molecular functions and genes previously reported in human IS using 3′-biased microarrays [6, 11]. These include: actin cytoskeleton signaling, CCR5 signaling in macrophages, NF-KB activation, a-adrenergic signaling, cellular growth and proliferation, cell death and survival, cell morphology, hematopoiesis, hematological system development and function and inflammatory response/disease [4, 5, 12, 13]. This study's small sample sizes preclude detailed interpretations of biological pathways. However, these pilot data suggest DAS involvement in IS and ICH pathophysiology which varies in ICH and in different IS etiologies.

Results suggest DAS differs in blood leukocytes following different cerebrovascular events. Due to the pilot nature of the study, and the lack of human transcriptome data following ICH, we will discuss only a few of the genes with differential exon usage in ICH. Among the genes that differentiated ICH were INPP5D (inositol polyphosphate-5-phosphatase) and ITA4 (integrin alpha 4). INPP5D is a regulator of myeloid cell proliferation and programming and was previously identified as correlating with increased tendency to hemorrhagic transformation of ischemic stroke [14]. ITA4 is involved in leukocyte recruitment [15] and leukocytes are intimately associated with IS and ICH [11]. For example, leukocytes are involved in clotting, and interact with injured vessels and brain following ICH and IS [11]. In addition, vascular endothelial growth factor (VEGF) signaling, which predisposes to hemorrhage because of new vessel formation [16], was implicated in ICH by several DAS genes, including NAV1 (neuron navigator 1), PDGFC (platelet derived growth factor C) and CCM2 (cerebral cavernous malformation 2). CCM2 mutations cause cerebral cavernous malformations leading to a predisposition for abnormal vessels and cerebral hemorrhage [17]. Interestingly, exosomes may be involved in ICH as evidenced by the differential expression of EXOSC1 (exosome component 1) and EXOSC9 (exosome component 9), coding for core components of the exosome complex [18]. Although exosomes have been implicated in neuroinflammation, neurodegeneration and cancer, they have not previously been associated with ICH [19, 20]. Finally, DGCR8 (microprocessor complex subunit) is involved in the biogenesis of microRNAs [21], thus suggesting an interplay between alternative splicing and miRNA in ICH.

REFERENCES

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It is understood that the examples and embodiments described herein are for illustrative purposes only and that various modifications or changes in light thereof will be suggested to persons skilled in the art and are to be included within the spirit and purview of this application and scope of the appended claims. All publications, patents, and patent applications cited herein are hereby incorporated by reference in their entirety for all purposes. 

1-4. (canceled)
 5. A method of differentiating between ischemic stroke (IS) from intracerebral hemorrhage (ICH), the method comprising: determining a level of exon or splice variant usage or expression of a plurality of biomarkers set forth in Table 1A, a plurality of biomarkers set forth in Table 1B, a plurality of biomarkers set forth in Table 1C, and/or a plurality of biomarkers set forth in Table 1D, in a biological sample from a patient, wherein detecting: a) an increase of the level of exon or splice variant usage or expression of a plurality of exons of the biomarkers set forth in Table 1A compared to a control indicates that the patient has suffered or is at risk of experiencing cardioembolic ischemic stroke (CE IS); b) an increase of the level of exon or splice variant usage or expression of a plurality of exons of the biomarkers set forth in Table 1B compared to a control indicates that the patient has suffered or is at risk of experiencing large vessel ischemic stroke (LV IS); c) an increase of the level of exon or splice variant usage or expression of a plurality of exons of the biomarkers set forth in Table 1C compared to a control indicates that the patient has suffered or is at risk of experiencing lacunar ischemic stroke (L IS); and/or d) an increase of the level of exon or splice variant usage or expression of a plurality of exons of the biomarkers set forth in Table 1D compared to a control indicates that the patient has suffered or is at risk of experiencing ICH; thereby differentiating between ischemic stroke (IS) from ICH.
 6. The method of claim 5, wherein the determining step is performed at 3 or more hours after a suspected ischemic stroke or ICH.
 7. The method of claim 5, wherein the determining step is performed at 3 or fewer hours after a suspected ischemic stroke or ICH.
 8. The method of claim 5, wherein the determining step is performed at 24 or fewer hours after a suspected ischemic stroke or ICH.
 9. (canceled)
 10. The method of claim 5, wherein the level of expression of the biomarker is determined at the transcriptional level. 11-13. (canceled)
 14. The method of claim 5, wherein the level of expression is determined by direct RNA sequencing of gene transcripts of the biomarkers.
 15. The method of claim 5, wherein the level of expression is determined by amplification of gene transcripts of the biomarkers.
 16. (canceled)
 17. The method of claim 15, wherein the amplification reaction comprises quantitative reverse transcription polymerase chain reaction (qRT-PCR).
 18. The method of claim 15, wherein the amplification reaction comprises reverse transcription (RT) followed by a ligase detection reaction (LDR) with single-pair fluorescence resonance energy transfer (spFRET) (RT-LDR/spFRET). 19-20. (canceled)
 21. The method of claim 5, further comprising the step of obtaining a biological sample.
 22. The method of claim 5, wherein the biological sample is blood, serum or plasma.
 23. The method of claim 5, wherein the increased level of exon usage of a biomarker is at least about 1.2-fold in comparison to a control.
 24. The method of claim 5, wherein the control is the expression level of the same biomarker in an individual with no history of stroke, heart attack, or peripheral vascular disease.
 25. The method of claim 5, wherein the control is a threshold level of expression representative of a population of individuals with no history of stroke, heart attack, peripheral vascular disease.
 26. (canceled)
 27. The method of claim 5, wherein the control is an individual or population of individuals who have increased expression of one or more biomarkers set forth in Table 1E. 28-29. (canceled)
 30. The method of claim 5, wherein the subject has experienced or is suspected of having experienced ischemic stroke or ICH. 31-35. (canceled)
 36. A solid support comprising a plurality of oligonucleotide probes that hybridize to a plurality of the biomarkers set forth in Table 1A, Table 1B, Table 1C and/or Table 1D. 37-43. (canceled)
 44. A reaction mixture comprising one or more primer pairs or a set of primers for amplifying one or more exons of a plurality of the biomarkers set forth in Table 1A, Table 1B, Table 1C and/or Table 1D.
 45. The reaction mixture of claim 44, further comprising one or more primer pairs or a set of primers for amplifying one or more exons of a plurality of the biomarkers set forth in Table 1E. 46-51. (canceled)
 52. A kit comprising a set of primers for amplifying one or more exons of a plurality of the biomarkers set forth in Table 1A, Table 1B, Table 1C and/or Table 1D.
 53. (canceled) 